fermentation technology research papers

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• v.22(5); 2021 May 5

Fermentation for future food systems

Ting shien teng.

1 School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore City Singapore

2 Food Science and Technology Programme, Nanyang Technological University, Singapore City Singapore

Yi Ling Chin

Kong fei chai, wei ning chen.

Modern biotechnology holds great potential for expanding the scope of fermentation to create novel foods and improve the sustainability of food production.

The growing human population and global warming pose an impending threat for global food security (Linder, 2019 ). This has prompted a critical re‐examination of the food supply chain from producers to consumers in order to increase the overall efficiency of food production, storage and transport. Much research in plant science consequently aims to increase production with new, high‐yield crop, fruit and vegetable varieties better adapted to changing climatic conditions. Yet, there is also much room for improving food safety by minimising food losses and recycling waste, valorising by‐products, improving nutritional value and increasing storage time. This is where fermentation comes in as a cost‐efficient, versatile and proven technology that extends the shelf life of food products and enhances their nutritional content. Moreover, there is enormous potential in fermentation to further increase efficiency and product range and even create new food products from non‐food biomass.

… there is enormous potential in fermentation to further increase efficiency and product range and even create new food products from non‐food biomass.

In a broader sense, fermentation can be defined as the cultivation of microorganisms such as bacteria, yeasts and fungi to break down complex molecules into simpler ones, notably organic acids, alcohols or esters. In a practical sense, it is one of the oldest food processing technologies to increase storage life along with cooking, smoking or air‐drying: fermentation was already fully industrialised for producing beer and bread millennia ago in ancient Mesopotamia and Egypt. It is also an elegant and simple technology as these microorganisms do most of the work without much human involvement.

Louis Pasteur’s discovery that microorganisms cause fermentation laid the basis for further improvement of the technology from traditional spontaneous fermentation to the use of defined starter cultures. Fermentation is now widely used to produce alcoholic beverages, bread and pastry, dairy products, pickled vegetables, soy sauce and so on. More recent advances based on genomics and synthetic biology include precision and biomass fermentation to produce specific compounds for the food and chemical industry or medicinal use. This is not the limit though: when combined with genomics, fermentation has even greater potential for creating novel foods and other products.

Untapped potential of an old technology

Such further improvements require a much better understanding of the microbes involved in fermentation processes and their metabolic capabilities and their interactions. For instance, the industrial robustness of lactic acid bacteria (LAB)—commonly used in cheese and yoghurt production—is due to differential expression of stress response genes that protect against environmental stresses (Smid & Hugenholtz, 2010 ). Identifying these genes and analysing their interaction with lactic acid production could help to determine the environmental factors that LAB respond to and use this knowledge to induce overproduction of lactic acid. To this end, genomics and metagenomics studies have used high‐throughput sequencing (HTS) to analyse the microbial communities in fermented food so as to identify desirable strains and characteristics. This would not only help to increase efficiency and production but also selection of strains that generate specific metabolites for a more complex flavour or texture profile. By way of example, genomics research has identified genes involved in proteolysis and amino acid conversion in LAB as a basis for generating specific flavour molecules from amino acids (Smid & Hugenholtz, 2010 ).

Even though fermentation was originally applied to preserve food through overproduction of acid or alcohol—the intoxicating effect of the latter was a welcome side effect—there are still inherent risks involved, in particular when using traditional or spontaneous fermentation. Pathogenic microorganisms or harmful metabolites can spoil the final product and present health risks for consumers. The application of genomic analysis would therefore help to increase safety by early detection of harmful microbes. Lastly, the combination of genomics and synthetic biology to rationally design desirable characteristics holds great promise for using non‐food biomass to generate wholly new food products that are safe, wholesome and appealing to consumers (Figure  1 ).

Refining traditional fermentation

With the advent of refrigeration, extended shelf life was no longer the main reason for fermenting food, yet these products remain hugely popular owing to their complex taste, texture and consumer demand for natural products with potential health benefits. Fermented food products still occupy whole supermarket shelves: beer and wine, kimchi, cheese, yoghurt, soy sauce, lemonade, and so on. These are all produced by traditional fermentation that either uses microorganisms naturally present on the substrate—wild yeasts that grow on grapes for instance—or controlled fermentation with a starter culture, or through so‐called backslopping by using a small amount of a previous fermentate to inoculate fresh substrate. Some of the desired outcomes include probiotics, phytochemicals, short‐chain fatty acids, peptides, vitamins and amino acids with antihypertensive, blood glucose‐lowering, anticancer and anti‐obesity properties (Leroy & De Vuyst, 2014 ; Chai et al, 2020 ). As sugars are converted into other metabolites, fermented foods are also considered low‐caloric.

Moreover, fermentation creates a complex taste and texture profile from amino acid and lipid degradation, extracellular polysaccharide production or mycelium growth. For instance, tempeh production starts with adding Rhizopus oligosporus to soybeans to break down antinutritional factors while increasing nutritional content. The fungal biomass remains in the final product and contributes to its flavour and texture. Similarly, different microorganisms also create the complex texture, taste and smell experience of a Stilton cheese or a Riesling wine.

… fermentation creates a complex taste and texture profile from amino acid and lipid degradation, extracellular polysaccharide production or mycelium growth.

Large‐scale production of fermented foods commonly employs the use of starter cultures: a collection of one or more microorganisms—such as Saccharomyces , Lactobacillus, Lactococcus, Streptococcus or Enterococcus —to inoculate the substrate. Starter cultures enable control over and predictability of the otherwise random nature of fermentation to improve food safety and standardisation. Primarily, starter cultures provide the food substrates with the necessary microorganisms required for propagation and colonisation even before fermentation begins. LAB for instance rapidly increase acidity and thereby inhibit undesirable microbes from growing. Similarly, Saccharomyces produces alcohol that inhibits other microorganisms. Starter cultures also confer important functions such as bacteriophage immunity, exopolysaccharide formation or amino acid biosynthesis, which prevent spoilage and improve flavour and texture of the fermented products. Again, better knowledge of the metabolic capabilities of the organisms involved would help to improve any of these aspects.

Despite the advantages of using starter cultures, many artisanal and small producers still prefer spontaneous fermentation by microbes from the environment. The presence of multiple species and strains has further potential for symbiotic utilisation of different metabolic pathways, which results in improved sensorial properties. Furthermore, indigenous microbiomes have a highly diverse gene pool along with adept metabolic functions which can provide beneficial effects. For instance, the bacterial populations collected from artisanal doenjang, a fermented soybean paste, are more complex than those collected from its commercial counterparts (Nam et al, 2012 ).

However, an undefined starter composition introduces large variabilities to the fermentation process. The final composition of the microbiota heavily depends on the environmental conditions, such as temperature, pH or salinity, and it can result in batch‐to‐batch variations when conditions change. Spontaneous fermentation inevitably results in inconsistent quality and can lead to the growth of undesirable or even pathogenic microorganisms. It is therefore crucial to refine both spontaneous and inoculated fermentation to increase predictability and safety.

As the rapid development of sequencing technology has considerably lowered sequencing cost and led to a rising number of published genomes in public databases, genomic studies of food microbial communities have advanced extensively. Metagenomic analysis using HTS may help to unveil the metabolic functions and parameters that affect the fermentation process such as substrate usages, enzyme production or metabolic outputs. Metabolic modelling coupled with flux balance analysis could then enable simulation of microbe growth and metabolite production in response to changes in the culturing environment (Alkema et al, 2016 ).

However, it is important to note that information from HTS reveals only the potential metabolic functions by the genes encoded, but these may not necessarily be expressed during fermentation. Metatranscriptomic analysis to complement genomic analysis reveals a more accurate picture of the metabolic activities. For instance, metabolomics, metagenomics and metatranscriptomic predicted that kimchi LAB had high metabolic capacities in a heterotrophic lactic acid fermentation process and that the fermentation was affected by bacteriophage infection (Jung et al, 2014 ). Altogether, metabolic analysis and modelling would not only help to improve yield, taste or texture in industrial‐scale fermentation based on starter cultures, but could also benefit smaller, artisanal producers to avoid contamination or spoilage by suppressing the growth of unwanted microbes or metabolic functions.

…metabolic analysis and modelling would not only help to improve yield, taste or texture in industrial‐scale fermentation based on starter cultures, but could also benefit smaller, artisanal producers to avoid contamination or spoilage…

Innovation through precision fermentation

Many food additives, such as enzymes, vitamins or natural food colouring, are produced by microbial fermentation. By way of example, riboflavin or vitamin B2 is produced by fermentation with the fungus Ashbya gossypii; the major source of rennet for cheesemaking are genetically modified bacteria; vitamin C is now produced by a combination of fermentation with Pantoea agglomerans and Aureobacterium and further chemical synthesis. Targeted fermentation to cheaply produce large amounts of a specific compound has helped to revolutionise the food industry, but it also creates many by‐products, which lowers the production efficiency and increases the difficulty of downstream purification.

Targeted fermentation to cheaply produce large amounts of a specific compound has helped to revolutionise the food industry…

One approach to minimise by‐product formation is generating synthetic cell factories where all available resources are diverted to produce the desired compounds and little else. Termed as precision fermentation or synthetic biology, the technology is now heralded as a potential substitute for traditional fermentation. At its heart is the engineering of optimised metabolic pathways and assembling the genes involved in a microbial chassis. This technology relies heavily on an extensive understanding of the microbial genomes and metabolic functions and requires a whole range of technologies such as artificial intelligence, bioinformatics, systems biology and computational biology for analysis and functional characterisation.

Starting with human insulin production by recombinant Escherichia coli bacteria in the 1980s, fermentation by genetically modified organisms to produce non‐microbial products has been extensively used by the food industry. This is especially obvious in the protein industry, where engineered microbes now produce substances that originally came from animals, such as whey, rennet or casein. Another prominent example is Impossible Foods, which uses soy leghemoglobin produced by an engineered yeast Pichia pastoris to give its plant‐based burger the flavour and colour of animal meat.

By pushing the boundaries of precision fermentation further, it is possible to envision future food production systems in which fermentation takes a central role to generate a wide range of food ingredients. An example is in the case of oleaginous red yeast Rhodosporidium toruloides which has been engineered to improve its natural synthesis of lipids and carotenoids as well as novel compounds that are industrially relevant (Park et al, 2018 ). Further engineering has now generated strains that export carotenoids from the cell for easier extraction and separation (Lee et al, 2016 ). Many start‐up companies are now developing engineered microorganisms to manufacture a wide range of food compounds. These and other innovations will inevitably have an even greater impact on the food industry.

Utilising other sources

An in‐depth understanding of the metabolism of the microbial community would also enable the exploitation of new substrates, in particular by‐products and waste from the food industry, to create higher‐value products. Research groups have demonstrated the value of fermentation of food wastes, such as okara and brewers’ spent grains, by probiotic bacteria Bacillus subtilis, to create new food products with increased nutritional value (Mok et al, 2019 ; Tan et al, 2019 ). The CRUST Group, a company in Singapore, collects unused and unsold bread from bakeries and restaurants as substitute for malted barley: the sugars are extracted as wort and fermented to “bread ale”. Efforts have also been made to valorise the seed of an exotic fruit, rambutan by fermenting, drying and roasting the fruit pulp and seed in a manner similar to cocoa bean processing to produce a cocoa powder‐like product (Chai et al, 2019 ). These and other uses show that fermentation can become an important solution for sustainable food production by converting food waste and by‐products into food products.

Utilising novel feedstock sources for fermentation can also help to meet increasing consumer preference for plant‐based diets; companies are already developing alternatives to traditionally fermented dairy products such as cheese and yogurt using soy and cereals. Generally, the combination of unconventional substrates and microbial strains could give rise to novel fermented foods with enhanced nutritional content and improved organoleptic properties.

An even more sustainable strategy is biomass fermentation for protein production based on microorganisms’ abilities to rapidly multiply under optimum conditions and produce a very high protein content of more than 50% dry weight. The resulting whole‐cell biomass can be served directly or blended with other food ingredients. Examples of such products include Marmite made from yeast extract, fermented bean paste and, more recently, the mycoprotein from a filamentous fungus, Fusarium venenatum , which is used as the base for meat analogues (Berka et al, 2007 ). The added benefit of the latter is the textural quality that mimics the fibrous structure of meat products and leads to an acceptable taste sensation. From a genomics point of view, single‐cell protein production could be comparatively easily explored by high‐throughput strain screening, adaptation and engineering to engineer microbial strains and cell factories for protein production.

Compared to other meat alternatives, such as cultured meat, biomass fermentation would be more efficient as it can use a much wider range of nutrients and feedstock. In fact, many complex and inexpensive feedstocks such as agricultural or industrial waste products can be valorised given the ability of many microorganisms, especially filamentous fungi, to metabolise any substrates. As such, biomass fermentation not only helps with meeting increasing demand for protein‐rich food but also benefits the environment by recycling waste. In terms of nutrition and health, it generates food products with lower cholesterol, fat and sugar levels and higher fibre content. One study explored the fermentation of okara by Rhizopus oligosporus and demonstrated improved nutritional composition (Gupta et al, 2018 ); other studies showed that proteins produced from biomass fermentation are better accepted by consumers than plant‐based meats due to their greater resemblance to animal meat (Souza Filho et al, 2019 ). Biomass fermentation is therefore an attractive alternative to supplement or substitute our dependence on animal proteins, while at the same time lowering carbon footprint and increasing nutritional value.

… biomass fermentation not only helps with meeting increasing demand for protein‐rich food but also benefits the environment by recycling waste.

Enhancing food safety

The use of fermentation to preserve food remains an important objective to date. Multiple mechanisms work together to prevent the spoilage of food which can be generally classified into two themes: competitive exclusion of spoilage microbes and the creation of an inhibitive environment with each influencing the other. Fermentative microbes release large amounts of compounds which includes lactic acid, alcohol or acetic acid, that inhibit the growth of other microbes. Fermentative microbes, on the other hand, are unaffected by these compounds and continue proliferating—a phenomenon termed amensalism.

However, improper fermentation may still present potential health hazards. Unhygienic conditions or inappropriate food handling may still lead to contamination and spoilage. Furthermore, spontaneous fermentation involving undefined indigenous microbiota carries the risk that undesirable or even pathogenic microorganisms expand and cause food‐borne diseases.

The first step to ensure food safety in fermentation is to identify the presence of such microbes and prevent their propagation. Besides quality assurance, constant observation also enables early intervention at the first indication of spoilage or contamination. Metagenomics and HTS along with bioinformatics now allow quick and accurate monitoring of whole microbial communities. Metabolomics and metagenomic analysis can further detect harmful metabolites and pinpoint the microorganisms responsible for producing them.

While it is easy to say that genome sequencing is the solution to spoilage, the reality is more complex and it requires long‐term observation and continuous examination of what constitutes wanted and unwanted microbes. One way would be to simply focus on known pathogens, but that depends heavily on a profound knowledge of good and bad microbes. Another approach is to look out for virulence genes or genes with deleterious effects. Yet, the presence of genes may not necessarily translate to expression. While it is a promising approach generally, using metagenomics to ensure food safety has still a long way to go.

While it is a promising approach generally, using metagenomics to ensure food safety has still a long way to go.

Approaching the problem from another angle, genomic analysis may be useful for identifying microorganisms producing, or with the potential to produce, inhibitive compounds that are safe for human consumption but restrict the growth of spoilage microbes. These notably include bacteriocins, peptidic toxins with potent antimicrobial properties. One prominent example is nisin, which is used as a food preservative to prevent bacterial contamination. Such compounds are thought to be safer than antibiotics because they are produced naturally in food and can be inactivated by trypsin and pepsin to protect the gut microbiota. Microbes encoding genes for bacteriocins are already actively identified for creating synthetic strains that secrete larger amounts of these natural preservatives or for conjugating strains from various sources into a single strain. To supplement food products with bacteriocins requires separate preparation of producer strains in industrial fermenters, followed by recovery and purification. In comparison, in situ production offers similar effects but at lower costs.

Protective bacteriocinogenic cultures may even serve as an alternative for long‐term storage of non‐fermentable foods. Importantly, the physiochemical and organoleptic properties of the food should not be affected throughout the process. In addition to selecting suitable strains to produce bacteriocins, an extensive understanding of the metabolic activities is necessary to ensure that the by‐products of microbes’ metabolisms will not affect the properties of the food product. Metagenomics analysis would again help to select the optimal microbe composition, environmental conditions and specific strains.

Implementation

To bring an innovation from laboratory to fork is an arduous task that requires considerable time and investment to make sure the final product is safe and accepted by consumers. Take the case of cultured meat, which is based on tissue engineering. It should be perceived as safe given that tissue engineering has been safely used in surgical implantations for decades. Yet when the technology is applied in food production, new concerns on food safety and consumer acceptance must be addressed. These hurdles that might deter the acceptance of cultured meat would be same for all other food innovations.

As with any regular food products, food safety is always a top concern for consumers and regulators. Fermented food products are no exception. While fermentation technology has been widely applied, there could be large variances across batches—or even contamination by pathogenic microbes or harmful metabolites—due to the heterogeneous nature of microbe compositions, metabolic processes and substrates. Therefore, stringent risk assessments of the final products are crucial for mitigating such risks before the new product is brought to the market.

The food risk analysis framework as proposed by the Food & Agricultural Organisation (FAO) has four steps: hazard identification, hazard characterisation, exposure assessment and risk characterisation, followed by risk management and risk communication. Novel food products can similarly be assessed under the same framework. However, given the differences between fermented foods in comparison with regular foods, additional assessments would be recommended for long‐term health effects since regular consumption over extended periods can lead to gradual accumulation of metabolites in the human body.

Consumer acceptance will remain an important and major factor that determines whether a novel food innovation will eventually be successful and consumers are generally receptive towards trying new tastes and flavours. But the same cannot be said for novel foods produced by unique technologies. Traditional fermentation may have been around for millennia, but precision fermentation may hit consumer rejection. The general perception towards precision fermentation is that of an artificial process; and when synthetic biology is involved, the technology becomes negatively associated with the prejudicial impression of genetically modified (GM) foods.

Traditional fermentation may have been around for millennia, but precision fermentation may hit consumer rejection.

However, synthetic biology has been around in the food space and food processing for a long time. For instance, chymosin, a coagulant in cheesemaking, was initially obtained from the lining of calves’ stomachs, but with increasing demand for cheese, calves’ rennet was displaced by fermentation‐produced chymosin (FPC) from genetically modified E . coli and yeasts. This example provides a suitable message for applications of synthetic biology in food processing: precision fermentation is a technique for producing naturally occurring products, such as enzymes and metabolites, that are not meant for direct consumption. There is fundamentally no difference in the product synthesised naturally and via GM technology, except that the latter achieves superior yield and purity. To encourage consumers to accept the products of precision fermentation would perhaps require more information and education on the process and how synthetic biology is only a means to an end.

Even though fermentation has been used for millennia, there is still tremendous untapped potential and endless possibilities for new applications in our current food systems—from fermentation‐derived ingredients to novel protein sources and foods using unconventional feedstock. From a health perspective, fermented foods have desirable characteristics for human health owing to probiotics or diverse bioactive compounds. In addition, with biomass fermentation as an efficient alternative protein source, we can potentially lower the costs of protein production and help millions of people out of malnutrition. There are also positive environmental effects owing to the reduced demand for livestock, which helps to decrease greenhouse gas emissions and pollution while saving land, water and animal feed. Channelling the ability of microorganisms to synthesise specific molecules through precision fermentation also allows the inexpensive and large‐scale production of virtually any ingredient for the needs of the food or the chemical industry.

Microorganisms show great promise as cell factories, but it is only through deploying various “omics” tools and synthetic biology that we can improve these to obtain the desired product properties and ensure predictability of an otherwise random fermentation. Through strain selection, screening and engineering, coupled with relevant risk assessments, the vast biodiversity of microorganisms can be explored to create novel and safe fermented products that can benefit human health and the environment. Though fermentation is one of the oldest technologies developed by humans, its potential for further improvement is far from limited.

Acknowledgements

This work was supported by the Food Science and Technology Programme, Nanyang Technological University, Singapore.

EMBO reports (2021) 22 : e52680. [ PMC free article ] [ PubMed ] [ Google Scholar ]

• Alkema W, Boekhorst J, Wels M, van Hijum SA (2016) Microbial bioinformatics for food safety and production . Brief Bioinform 17 : 283–292 [ PMC free article ] [ PubMed ] [ Google Scholar ]
• Berka RM, Nelson BA, Zaretsky EJ, Yoder WT, Rey MW (2007) Genomics of Fusarium venenatum : an alternative fungal host for making enzymes . Appl Mycol Biotechnol 4 : 191–203 [ Google Scholar ]
• Chai KF, Chang LS, Adzahan NM, Karim R, Rukayadi Y, Ghazali HM (2019) Physicochemical properties and toxicity of cocoa powder‐like product from roasted seeds of fermented rambutan ( Nephelium lappaceum L.) fruit . Food Chem 271 : 298–308 [ PubMed ] [ Google Scholar ]
• Chai KF, Voo AYH, Chen WN (2020) Bioactive peptides from food fermentation: a comprehensive review of their sources, bioactivities, applications, and future development . Comp Rev Food Sci Food Saf 19 : 3825–3885 [ PubMed ] [ Google Scholar ]
• Gupta S, Lee JJL, Chen WN (2018) Analysis of improved nutritional composition of potential functional food (okara) after probiotic solid‐state fermentation . J Agricult Food Chem 66 : 5373–5381 [ PubMed ] [ Google Scholar ]
• Jung JY, Lee SH, Jeon CO (2014) Kimchi microflora: history, current status, and perspectives for industrial kimchi production . Appl Microbiol Biotechnol 98 : 2385–2393 [ PubMed ] [ Google Scholar ]
• Lee JJL, Chen L, Cao B, Chen WN (2016) Engineering Rhodosporidium toruloides with a membrane transporter facilitates production and separation of carotenoids and lipids in a bi‐phasic culture . Appl Microbiol Biotechnol 100 : 869–877 [ PubMed ] [ Google Scholar ]
• Leroy F, De Vuyst L (2014) Fermented food in the context of a healthy diet: how to produce novel functional foods? Curr Opin Clin Nutr Metab Care 17 : 574–581 [ PubMed ] [ Google Scholar ]
• Linder T (2019) Making the case for edible microorganisms as an integral part of a more sustainable and resilient food production system . Food Security 11 : 265–278 [ Google Scholar ]
• Mok WK, Tan YX, Lee J, Kim J, Chen WN (2019) A metabolomic approach to understand the solid‐state fermentation of okara using Bacillus subtilis WX‐17 for enhanced nutritional profile . AMB Express 9 : 60 [ PMC free article ] [ PubMed ] [ Google Scholar ]
• Nam YD, Lee SY, Lim SI (2012) Microbial community analysis of Korean soybean pastes by next‐generation sequencing . Int J Food Microbiol 2 : 36–42 [ PubMed ] [ Google Scholar ]
• Park Y‐K, Nicaud J‐M, Ledesma‐Amaro R (2018) The engineering potential of Rhodosporidium toruloides as a workhorse for biotechnological applications . Trends Biotechnol 36 : 304–317 [ PubMed ] [ Google Scholar ]
• Smid EJ, Hugenholtz J (2010) Functional genomics for food fermentation processes . Annu Rev Food Sci Technol 1 : 497–519 [ PubMed ] [ Google Scholar ]
• Souza Filho PF, Andersson D, Ferreira JA, Taherzadeh MJ (2019) Mycoprotein: environmental impact and health aspects . World J Microbiol Biotechnol 35 : 147 [ PMC free article ] [ PubMed ] [ Google Scholar ]
• Tan YX, Mok WK, Lee J, Kim J, Chen WN (2019) Solid state fermentation of brewers’ spent grains for improved nutritional profile using Bacillus subtilis WX‐17 . Fermentation 5 : 52 [ Google Scholar ]

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• Published: 19 April 2023

The microbial food revolution

• Alicia E. Graham 1 &
• Rodrigo Ledesma-Amaro   ORCID: orcid.org/0000-0003-2631-5898 1  

Nature Communications volume  14 , Article number:  2231 ( 2023 ) Cite this article

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• Applied microbiology
• Industrial microbiology

Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.

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Introduction.

The current food systems have been pushed to a crisis, as they struggle to keep up with nutrition and protein demand coupled with population growth 1 . All our food systems—agriculture, animal husbandry and aquaculture—are grappling with the degradation of land, climate change and climate disasters, which are set to rise in the future 2 . Although moving towards plant-based foods is less environmentally harmful, it still relies on climate or season and intensive land, water and chemical use 3 . The time for a microbial revolution in food is ripe as microorganisms have the potential to enhance, improve or even replace the currently available alternatives 4 , 5 . They have been proven to be an ecological and resilient food source, especially when compared to traditional protein sources such as meat 6 , 7 . Genetic and system design can advance sustainability further when renewable and waste feedstocks are considered 8 , 9 . Furthermore, they are highly resilient due to their decentralised nature that does not rely on location limitations, such as temperature or weather 10 . Finally, they also have a high nutritional profile 11 , crucial in the face of rising diet-related health epidemics.

Microorganisms are no stranger in the history of food; however, research has lately revealed the vast array of health benefits and ecological savings that can be derived from using microorganisms in food 12 , 13 . This has led to an explosion in new applications, improvement in traditional practices using state-of-the-art technology 14 , 15 , 16 and a better understanding of their roles and benefits 13 . Fermentation can be used both directly on foods to improve nutrition, taste or texture 17 , 18 , as well as used as a production platform to produce value-added ingredients in the food industry 19 , 20 , 21 . Moreover, using fermentation to produce microbial biomass as a nutritional food source is starting to be adopted in both animal feed and human foods 22 , 23 , 24 . However, there are challenges to overcome in each of these applications, including scalability and economic or ecological sustainability. Novel tools can be applied to these fields to enhance and accelerate the development of microbial-based foods and overcome current limitations. This includes high-resolution and high-throughput characterisation of microorganisms 14 , 25 , as well as genetic and metabolic engineering tools 4 . By engineering and selecting strains, it is possible to improve flavour 26 and nutrition 20 , 27 , 28 as well as increase sustainability using waste feed or cheap non-competing carbon sources 8 , 29 . This can contribute to increasing applications and uptake to propel a microbial revolution in food.

Due to the high potential and varied applications of microbes in food, there have been numerous recent start-ups in this space, ranging from improving traditional fermentation to creating new products (Table  1 ). Development is still needed for technical advances and consumer acceptance but the field of single-cell proteins and engineered microbes in food has high potential, as will be explored in this review. This review aims to give an overview of the different applications of microorganisms in food ranging from traditional fermentation techniques to biotech applications of ingredient production (see Fig.  1 ). It covers the different novel applications of microbes in the food system as well as the role of synthetic biology in advancing this field. Finally, the obstacles and future perspectives will be considered.

A view of the various applications that rely on microbial processes. State-of-the-art in each process is explained as well as the current or potential role of genetic engineering and other future developments to enhance the process or use.

The use of microbes in food

Rise of fermentation in history.

Microorganisms were first leveraged by humans in the food system for fermentation. Fermentation is one of the earliest known food technologies dating as far back as 7000BC or earlier and arising independently in multiple ancient cultures 30 , 31 . Alongside smoking and salting, fermentation was a primary method of food preservation and thus a crucial technology in the rise of human civilisations 32 . In addition, the process also introduced many new products, flavours and tastes. Different fermented products rose from specific environments and conditions which produced a diversity of edible products 32 . These include, but are not limited to, dairy products such as cheese and yoghurt, alcoholic products such as beer and wine, fermented bean products such as soy sauce, douchi (豆豉) and natto, other vegetables such as sauerkraut and kimchi and many more 32 .

The advent of new processing and preservation methods such as refrigeration, the use of natural and artificial preservatives, and freezing and vacuum sealing, among others, have provided alternatives to traditional fermentation. However, more recently, research has brought to our attention the many health benefits offered by a microbial presence in food 13 , 33 , causing a resurgence in popularity, and many newly popularised health foods are fermented or have fermented ingredients. This is compounded by the rise of plant-based diets and increasing access to international foods—many of which include traditionally fermented products. A good example is Kombucha, a traditional Manchurian fermented tea drink which was introduced to the international market with many purported health benefits and now is valued at over 1 billion US dollars 34 . Other well-known examples are Tempeh and Tofu, two fermented soybean products from Indonesia and China, respectively, which are now consumed as meat-alternative protein sources globally 35 .

Different functions and health benefits of fermented foods

Fermentation, in the context of food, refers to raw material undergoing enzymatic conversions in the presence of microorganisms 13 , 36 . These conversions result in alteration in their physicochemical properties. Many of the resulting metabolites play an active role in food preservation, inhibiting the growth of contaminating or spoiling pathogens and increasing shelf life, but others contribute to nutrition, texture, taste and smell 13 . Depending on their composition, fermented food may also bring health benefits. The list is a brief summary of some of the most relevant benefits, although comprehensive reviews can be found on the topic 18 , 37 :

Microbiome enhancing (or probiotic) qualities: The gut microbiome is increasingly proving to be crucial for maintaining health 38 . The use of probiotics supplements has become widely adopted, although the health benefit and strain formulation remain controversial topics 39 . The consumption of certain fermented foods themselves has proven to have probiotic and health-promoting effects 40 .

Increasing bioavailability of nutrients in food: This is due to microorganisms breaking food down for easier digestion and absorption of ingested nutrients. For example, lactic acid fermentation can increase the food’s iron content by optimising pH and acid content for solubility 41 . Similarly, fermentation can improve the nutritional value of food by interfering with anti-nutritional factors, which impede protein, carbohydrate or phytochemical availability. For example, trypsin inhibitors found abundantly in various cereals, grains and legumes have been shown reduced activities in fermented foods 42 .

Reducing Glycaemic Index: The Glycaemic Index (GI) measures how quickly carbohydrates in food raise blood glucose levels 43 . Probiotic and/or fermented cereals, pseudo-cereals and dairy products have been linked to a reduction in the GI of the food and the blood sugar response 43 , 44 . Lowering GI intake and response has been shown to reduce risk factors for diseases such as type II diabetes and cardiovascular disease 43 .

Removing toxins: Microbial consortia can also act by removing toxic compounds and inhibiting the growth of pathogenic species. For example, Aflatoxin, a common toxin found in foods contaminated with Aspergillus flavus , has been shown to be enzymatically reduced in various fermentative processes 45 . Free radicals in vegetable and fruit products are also reduced during fermentation 46 .

Biochemical pathways producing health-promoting compounds: Many microorganisms naturally produce nutritionally beneficial chemical compounds including but not limited to antioxidants, polyunsaturated fatty acids, conjugated linoleic acids (CLA), sphingolipids, vitamins and minerals 4 , 47 , 48 .

However, fermentation does not always improve the foods and undesired microorganisms can negatively impact some nutritional aspects. Some examples include the production of toxic biogenic amines by lactic acid bacteria 35 , including an increase of free histamine due to the high presence of histidine-producing enzymes ( l -histidine decarboxylase) in microorganisms 49 . To counteract this, strategies have been developed to either optimise strain selection 50 or use engineered strains to enhance biogenic amine degradation 51 . Finally, it is also worth noting that many health claims related to fermented foods are yet to be fully verified by randomised controlled trial studies and have often been exaggerated for marketing purposes 52 .

The nutritional profile of microbes

Microbial biomass itself also often has qualities that lend itself to consumption as food, including high protein, fibre and bioactive compound content (see Fig.  2 ).

The left panel shows the various components of microorganisms that are beneficiary for nutritional needs. This includes both macro-molecular elements such as proteins and fibre as well as small bioactive compounds. The right panel shows the relative levels of fibre, protein and micronutrients in four groups of microorganisms commonly used for food applications based on comparisons from the review by Ravindra 11 .

All microorganisms are generally characterised by high protein content, with algal species averaging between 40–60%, fungi 30–70% and bacteria averaging between 53 to as high as 80% 11 , 12 . Furthermore, many species are complete amino acid sources, containing adequate amounts of essential amino acids which humans cannot synthesise and need to acquire from diet 53 . In addition, many microbes have a high content of essential amino acids that are lacking in plants 54 .

Fibres, resistant carbohydrates that are key in maintaining gut health 55 , are also elevated in many microbial species 11 . Algae, for instance, has a high fibre content that is composed mainly of insoluble fibres, cellulose and other polysaccharides found in their cell walls 56 . Both filamentous fungi and yeast have potentially beneficial fibres, namely \({{{{{\rm{\beta }}}}}}\) -glucan and mannan-oligosaccharides, both of which are consumed as health supplements for gut health and immune-boosting effects 57 , 58 .

Although lipid content is generally low compared to animal products, oleaginous yeasts and algae are a source of high-value dietary lipids, especially long-chain polyunsaturated fatty acids 34 , 59 . Interestingly, the overall calorie content can be quite low, such as in commercially available nutritional yeast flakes, which contain 400 calories per 100 g, bringing a high ratio of nutrition to energy. Finally, microorganisms often have high endogenous contents of nutritionally relevant compounds, including vitamins, minerals, antioxidants and other functional ingredients 11 .

The nutritional profile of microorganisms requires further investigation as their use becomes more widespread. The true digestibility of the elements discussed above has not been fully elucidated 11 and the compositions can differ widely based on different species and the environments in which they are grown 60 . Species need to be carefully selected as some microorganisms also have significant safety and health detriments. An elevated RNA content is often seen in microorganisms which can lead to health issues, such as gout and kidney stones 61 . Some fungal and bacterial species also produce allergens and toxins and are thus ill-suited as food or require processing before ingestion 11 . By carefully choosing species, substrates, and conditions, the nutritional aspects of the food can be modulated to suit specific needs.

New technologies and applications for microbes in human food

Enhancing fermentation.

Fermentation can be optimised by specially selecting, breeding or engineering strains of microbes to enhance the appearance, taste or health profile of fermented foods 18 , 62 , 63 . Traditionally, breeding and selection techniques were used to select for favourable qualities even before the biology of microbes was discovered, leading to vastly different strains for specific uses 30 . Using genetic profiling techniques and -omics technology, we are now able to further identify strains with favourable properties 14 , 15 . Large-scale analysis has also enabled the identification of strains with desired aromas, which were further improved by hybridisation techniques 16 .

More recently, fermentation has been enhanced by using genetic engineering, where strains used in traditional fermentation can be manipulated to produce additional beneficial products. Some examples of modifications include the enhanced production of B vitamins in Lactobacilli used in dairy products 63 , 64 or the synthesis of aroma compounds in S. cerevisiae strains for novel and improved beer flavours 65 .

Genetic engineering has also been used to improve the sustainability of the fermentative food processes, which can be achieved by expanding or improving substrate range and utilisation 22 , 66 , 67 This furthers the potential to use waste feedstocks 8 , 9 and move towards a fully circular economy.

It is worth noting that many fermentation processes are carried out by microbial communities rather than single strains, which adds an additional layer of complexity to the understanding and limits our capacity to improve them. Advances in sequencing technologies and systems biology have allowed us to improve our knowledge of microbial consortia, including those found naturally in foods, as has been reviewed in previous works 68 , 69 . In addition, in the last years, synthetic biology tools specifically developed to engineer microbial communities have been created 70 , which have the potential to be used to improve food manufacturing. This includes spreading metabolic burden such as when two strategies to reduce browning in soy sauce production were engineered to act synergistically in two microbial species 71 , or enhancing natural coculture properties, such as increasing quorum sensing mechanisms which reduce food spoilage 72 .

Use of microbes as a protein source in human food

The use of microbes as a food ingredient is known as single-cell protein (SCP) and usually refers either to dried or processed microbe biomass or to the proteins extracted from it. It can be ingested either as a supplement, ingredient or as a main food source (see Fig.  1 ). Thanks to its potential for sustainable fermentation 8 , 28 and its favourable nutritional profile 11 , it has the potential to become a large component of our diet.

SCP has a long and varied history, beginning before the World Wars and continuing into the late and mid 20th century 73 , 74 . However, most projects were discontinued in the face of rising energy costs and the success of the green revolution, although some legacies remain 75 . One of the first of these is Marmite, established in 1902 as a by-product of the beer industry has even been consumed as an army ration as a source of B vitamins 61 . Since then, there has been development in other, more texturised SCPs—notably that of Quorn. Quorn, established in the 1980s, produces SCP from the filamentous fungi Fusarium venenatum and then treated to remove excess nucleic acid content and finally texturized to create meat replacements 76 . It is now a widely distributed product sold in 17 countries with a reported revenue of 236 million GBP in 2020. SCPs are also consumed as a health supplement, such as the microalgae Chlorella and Spirulina, which are rich sources of proteins as well as phytonutrients and vitamins 77 .

Given the ecological and nutritional benefits of SCPs, there is a renewed demand which has resulted in research into new sources of SCPs as well as novel cultivation methods. There is a profusion of start-up companies trying to bring new SCP products to market with some examples listed in Table  1 , with many start-ups focussing on meat alternatives.

So far, most research has focused on wild-type (non-engineered) strains, which have been selected based on their protein content and whose production have been optimised manipulating growing conditions. Synthetic biology has the potential to engineer selected strains to further improve protein production, which can be achieved by (1) enhancing and expanding the capacity to efficiently use desirable feedstocks, (2) improving yields for biomass and protein production and (3) adding functionalities to the single-cell protein by the co-production of valuable compounds such as vitamins or antioxidants 78 . Improving growth and substrate use can greatly improve ecological and economical aspects, for example, by transforming waste into proteins 79 .

Animal meat alternatives

Microbes are a promising substitute for meat products. This is thanks to their matching protein and nutrient levels, as well as their potential to be modified and texturized to resemble meat.

One of the most established companies is Quorn, which produces SCP derived from filamentous fungi. Quorn has products that resemble meat products from chicken nuggets to beef mince and has a large selection of different textures and forms it comes in refs. 80 , 81 . To achieve this, the long strands of hyphae are mixed with binding agents and then this fibre–gel complex is freeze texturised which allows for hyphal laminations that recreate the fibrous texture of meat 80 . Other start-ups including Meati Foods, Mycorena and Nature’s Fynd are also producing meat analogues from filamentous fungi.

Besides mimicking the nutritional profile or protein content, meat flavourings can also be produced by microbes. These products can be extracted and purified, or the whole microbial biomass can be used. For example, in the Impossible burger, Pichia pastoris is engineered to produce soybean leghaemoglobin c2 26 , which recreates part of the flavour profile of meat. The engineered microorganism is then incorporated with other ingredients including soy and potato proteins. Haemoglobin is also being produced as a stand-alone ingredient to add to plant-based meats, such as in the start-up Motif Foodworks. In academia, there is a concentrated effort to produce many variations of haemoglobin proteins which could account for future taste expansions 82 . Other individual components of meat can also be produced, such as the structural elements gelatine and collagen 83 , 84 .

Finally, one main challenge of recreating meat is providing an adequate lipid composition and content. Most plant-based alternatives utilise plant oils, which have a strongly differing taste and mouthfeel. The endogenous contents of lipids in microbes also differ significantly from that of meat; however, there is vast academic research on producing dietary lipids in microbes. Oleaginous species have been found to be a suitable production platform for highly nutritious fatty acids, such as omega-3 fatty acids which are found abundantly in fish 27 . Furthermore, advancement in the production of microbial oils gives us the potential to not only tune lipid composition but to also modify fatty acids to become more suitable for animal replacement uses 85 . Little focus has been given to mimick animal fats in academic research, although start-ups such as Melt & Marble and Nourish Ingredients aim to make dietary fats for animal replacements through fermentation.

Other animal product alternatives

Engineering microbes also have the potential to recreate animal products such as dairy and eggs. This is done through precision fermentation, where the pathways of individual components have been engineered into microorganisms.

Milk is composed of oligosaccharides, fats, sugars and proteins, primarily that of casein and whey 4 . These various components are being reproduced using synthetic biology in microorganisms 4 . The main milk proteins, namely casein proteins and whey proteins, have been successfully engineered into various organisms, including bacteria and yeasts 4 . These technologies are being employed by various start-ups developing animal-free milk, such as Perfect day, Better Dairy and Formo, which use purified milk proteins extracted from microbial cell factories and mixed with other fats and sugars.

Human breast milk has also been researched as it is thought to have important effects on the development of the neonatal gut flora and immune system 86 . Components such as milk fats and milk oligosaccharides have been developed with precision fermentation for human breast milk, both in academia as well as in industry, such as by the SME Conagen. Human milk oligosaccharides (HMOs) have been produced in both S. cerevisiae and B. subtilis 87 and human milk fats in the oleaginous yeast Y. lipolytica 88 . The probiotic effects can also be mimicked by recreating the microbiome of breast milk through the addition of microbial populations to formula 89 . The actual effects of these supplements would benefit from further studies in humans.

Eggs have a larger and more complex group of proteins that are responsible for their unique texture and taste. However, there have been efforts to recombinantly express different proteins, initially for allergenicity and protein studies 90 , 91 , and more recently as food ingredients 92 , 93 . Furthermore, there have also commercial efforts to produce egg alternative products made up of multiple egg proteins. This includes the start-up EVERY, which launched an egg white product made from recombinantly produced proteins in 2021.

One animal-based ingredient that has already been largely replaced by precision fermentation is rennet, an enzyme mixture containing chymosin found in the lining of the stomach of young ruminants. Commercial chymosin is now mostly produced in Aspergillus niger , which has allowed many kinds of cheese to become suitable for vegetarians as well as reducing the price, benefiting cheese makers 94 .

Microorganisms in animal feed

The use of microbes in animal feed first appeared over a century ago when brewery by-products were used to supplement feed by Max Delbruck. More recently, using microorganisms as a main or supplemental nutritional source has become established as an industry norm in both animal agriculture 95 and aquaculture 23 . This is due to an increase in regulatory ease and technological capabilities as well as growing pressures for cost and ecological efficiency 96 .

Many different microbial species have been investigated for the benefits in both animal health and production output 23 , 24 . Different microbial species each have their own limitations and advantages and thus need to be matched to desired functions and livestock 23 , 24 . Furthermore, there are different delivery options- including as a sole nutritional source 23 , as nutritional additive 24 or can act as probiotics 97 , 98 .

Live microbial supplements can act as probiotics and can either be species delivered to colonise the gut and integrate to improve the existing microflora, or to help balance the existing microbiota by modulating the pH, feed existing microorganisms and to defend against pathogenic species. Using probiotics in animal feed is becoming an industry norm as it has large therapeutic gains while reducing the need for drugs and antibiotics. In addition, the use of probiotics is shown to improve feed uptake, immune response and stress tolerance 97 , 98 , 99 . It has also been linked to increased growth, biomass and milk production 97 .

The new generation of SCP-based animal feed uses engineered microorganisms nutritionally tailored to the target animal 28 , 78 , 100 . Moreover, it can be also employed as a nutraceutical and therapeutic platform such as in the previously commercial omega-3 enriched Yarrowia biomass employed in Verlasso® salmon 101 , and the efforts in the start-ups such as Cyanofeed (see Table  1 ). Vitamins, fatty acids and phytonutrients have been successfully delivered through feed 28 . Finally, engineering organisms to utilise waste substances as carbon sources can greatly lower the ecological footprint of highly polluting animal agriculture industries 28 , 29 .

Precision fermentation of food ingredients and additives

One of the most developed uses of engineered microbes in our current food ecosystem is the production of ingredients and additives. For decades, microorganisms have been selected and improved to maximise the synthesis of molecules of interest, first by random mutagenesis and selection and then by genetic and metabolic engineering in a practice called precision fermentation 16 , 21 . A paradigmatic example is the production of vitamin B2, where chemical synthesis was substituted by fermentation in the 90s 102 . The yields and productivities of the processes are key to determining economic feasibility and therefore, metabolic engineering is playing an important role not only in increasing yields but also enabling the production of heterologous chemicals 22 . Interestingly, the use of genetically engineered strains to produce specific compounds is generally well accepted by consumers. This is because, by the end of the fermentation process, the molecules of interest are extracted and purified. They are therefore typically free of recombinant cells or DNA, allowing them to be labelled as natural products 103 .

While most nutraceuticals and additives with health benefits are still made by chemical synthesis or plant extraction, an increasing number of them are now bio-manufactured by microorganisms 4 . Some of these nutraceuticals include water-soluble vitamins (vitamin B complex and vitamin C) as well as fat-soluble vitamins (vitamin A/D/E and vitamin K) 20 . Other nutraceuticals made by engineered microbes have been reviewed elsewhere 21 , and the list includes omega-3 fatty acids, polyphenols such as resveratrol and naringenin, carotenoids such as beta-carotene or Astaxanthin, and non-proteinogenic amino acids such as GABA and beta-alanine. Other ingredients made by microbes are intended to improve the organoleptic properties of the food to which they are added to, improving taste, odour, colour and feel. Flavour enhancers such as glutamate (MSG), inosine monophosphate (IMP) and guanosine monophosphate (GMP) are made by microbes and contribute to the desired umami flavour 104 . Microbes have also been engineered to produce sweeteners such as stevia-derived molecules, xylitol or erythritol 105 , 106 , 107 . More exotic, hoppy flavours have been engineered into yeast to make tastier beer 65 . Odours and aroma compounds have been made by microbial processes like those of rose (2PE) 108 , orange/lemon (limonene) 109 , mint (menthol) 110 , peach (gamma-decalactone) 111 , among many others.

In addition, coloured molecules have been synthesised by microbes with the intention to be used as pigments for food and beverages. Some examples include orange (beta-carotene, canthaxanthin), red (lycopene, astaxanthin, prodigiosin), yellow (riboflavin), blue (phycocyanin), purple (violacein) and black (melanin) colourants 19 .

Obstacles and future perspectives

Technical obstacles.

To have a fully incorporated use of microbes in food, there are some technical difficulties that must be overcome. First, one of the main nutritional drawbacks is the high content of nucleic acids—namely RNA content. Ingestion of excessive quantities of nucleic acids particularly purines, increases the quantity of uric acid in the body which is a risk factor for gout and renal calculi as well as a strong risk factor for Metabolic Syndrome and cardiovascular disease 112 . This can be partially mitigated through processing methods, including heating and purification as employed by current single-cell protein manufacturers 113 , 114 . In the future, it would be possible to envisage an inducible method engineered into microbes to self-purify excess nucleic acids.

As a sole food source, the odours and textures of pure microbial cell mass have been postulated to be unsuited to human palate, however this setback could be improved through breeding or engineering in taste with genetic modifications or by creating mixtures or co-cultures to have novel and pleasant tastes 16 , 115 .

Many microorganisms, especially yeast, fungal and algal clades also have thick cell walls. In many cases, this is an important contributor of fibre in the diet. However, for some SCP, the thick cell wall can limit the number of nutrients that can be taken up and can itself be indigestible. Therefore, it may be necessary to treat the SCP using heat and/or mechanical and enzymatic processes, improving nutrient bioavailability 114 .

Food safety

Microbial-based foods and ingredients must go through regulatory approvals, which are stricter when new or engineered species are used. Regulatory bodies assess safety and authorize foods in a country-specific manner. For example, the FDA and EFSA are the main regulatory bodies in the USA and Europe, respectively. Some strategies to facilitate the obtention of approvals for microbial foods include the use of approved organisms and processes, limiting the application to animal feeding, purification of products, and removing foreign DNA and living cells.

The safety of the foods must also be considered for each different species. There has already been extensive investigation into some of the main target species that have confirmed their food safety both for fermentation, ingredient production and SCP use. Special attention must be paid to possible contamination in the process and to the potential production of endo and exotoxins that cause allergic and adverse reactions when ingested. Some toxins may be removed by simple heat or chemical treatments. However, through stringent strain selection 116 , strain engineering 117 and correct fermentation technologies, contamination and toxin production can be prevented or eliminated.

Consumer acceptance

One of the largest challenges of deploying single-cell proteins and genetically engineered microorganisms in food is consumer acceptance. Genetic modification is still under strict regulations, which differ between countries with some being particularly strict on introducing food with modified genetic information. Moreover, a large percentage of people still do not accept the idea of eating genetically modified materials. With the increasing awareness of improving the ecological aspect of diets 118 , this attitude might be changing as seen with the popularity with lab-grown meats and some synthetic meat and milk alternatives; however, these products are still uncommon in a commercial setting and therefore not incorporated in the average household’s diet.

To promote consumption, it is thus crucial to take the preparation and cultural context of microbial foods into account. Education and marketing can help counteract unfamiliarity and lack of consumption experience 119 . In addition, the design of microbial foods should consider the need to fulfil religious or cultural values, such as kosher or halal requirements 120 .

Economic barriers

A large problem of deploying SCP is the capital expenditure needed to expand the technologies and market the new food source. Maintenance costs and substrate usage also limit profitability. Because of the costs incurred for prototype development, one of the initial SCP projects by Imperial Chemical Industries (ICI) was abandoned when it failed to compete with cheap agriculture, especially with modified soybeans 10 . However, more recent technologies seem to suggest that building a plant for growing microbes could now be economically feasible 121 , which is facilitated by the optimisation of the growing conditions 122 , advanced fermentation technologies 123 , and higher yields achieved by engineered microbes 100 . Another economic barrier for commercialisation is the lengthy and expensive process associated with obtaining the necessary regulatory and safety approvals. Although dependent on price, variety and transportation, the employment of waste streams also has the potential to lower the process cost and simultaneously increase sustainability 10 . However, this is harder to introduce to the market as it is not fully understood whether the nutritional qualities of the product would be affected.

Taken together all the information discussed above, there is an obvious interest in developing more microbial-based foods and ingredients, as seen by the increased number of related academic publications, conferences, companies and commercial products. This is in part encouraged by the consumer demand for healthier and more sustainable foods.

Synthetic biology and microbial strain engineering broaden the horizons of microbial foods that can be designed, enabling the creation of desired nutritional profiles, aroma compounds, flavours and textures, all of which can build towards personalised nutrition (Fig.  3 ). To translate this technological capability into sustainable commercial products, the public perception of microbial foods must continue to change and the legislation must facilitate the implementation of these novel processes while maintaining high safety standards. The expansion and normalisation of microbial foods will increase production volumes, decreasing costs and optimising the efficiency of the technology. Reduced costs can then aid the development of microbial processes in less developed areas of the planet, which often need to improve nutrition. Looking at the future, engineered microbes are expected to play a role in delivering food where traditionally inaccessible, such as in disaster relief, deserts or even in space 124 , 125 .

A schematic showing the obstacles and future developments in the path to adopting widespread use of Microbial foods. In the beige circle the main obstacles are shown, including the economic viability of some processes, the consumer acceptance of some products, especially GMOs and, in some cases, the presence of undesired molecules. Future developments, shown in the blue arrow, aim to improve microbial-based foods and overcome these obstacles, and include producing nutritionally complete whole foods, alternatives to animal products (meat, dairy, eggs), and ingredients (like flavours or nutraceuticals) that can be made in an affordable and sustainable way, perhaps using waste or CO 2 as carbon sources.

In conclusion, if there is continued innovation and microbial foods are designed with sustainability and ethics in mind, they have the potential to revolutionise current food systems. This microbial food revolution could be key in designing future-proof strategies to face the health and environmental challenges of the future.

Rockström, J., Edenhofer, O., Gaertner, J. & DeClerck, F. Planet-proofing the global food system. Nat. Food 1 , 3–5 (2020).

Article   Google Scholar  

Change, I. C. Land: An IPCC Special Report on Climate Change. Desertification, Land Degradation, Sustainable Land Management, Food Security, and Greenhouse Gas Fluxes in Terrestrial Ecosystems 1–864 (IPCC, 2019).

Sun, Z. et al. Dietary change in high-income nations alone can lead to substantial double climate dividend. Nat. Food 3 , 29–37 (2022).

Article   CAS   Google Scholar  

Lv, X. et al. Synthetic biology for future food: research progress and future directions. Future. Foods 3 , 100025 (2021).

CAS   Google Scholar  

Choi, K. R., Yu, H. E. & Lee, S. Y. Microbial food: microorganisms repurposed for our food. Micro. Biotechnol. 15 , 18–25 (2022).

Humpenöder, F. et al. Projected environmental benefits of replacing beef with microbial protein. Nature 605 , 90–96 (2022).

Article   ADS   PubMed   Google Scholar  

Järviö, N., Maljanen, N. L., Kobayashi, Y., Ryynänen, T. & Tuomisto, H. L. An attributional life cycle assessment of microbial protein production: a case study on using hydrogen-oxidizing bacteria. Sci. Total Environ. 776 , 145764 (2021).

Javourez, U., O’Donohue, M. & Hamelin, L. Waste-to-nutrition: a review of current and emerging conversion pathways. Biotechnol. Adv. 53 , 107857 (2021).

Article   CAS   PubMed   Google Scholar  

Gao, R. et al. Enhanced lipid production by Yarrowia lipolytica cultured with synthetic and waste-derived high-content volatile fatty acids under alkaline conditions. Biotechnol. Biofuels 13 , 1–16 (2020).

Linder, T. Making the case for edible microorganisms as an integral part of a more sustainable and resilient food production system. Food Secur. 11 , 265–278 (2019).

Ravindra, P. Value-added food:: single cell protein. Biotechnol. Adv. 18 , 459–479 (2000).

Article   PubMed   Google Scholar  

Sharif, M. et al. Single cell protein: Sources, mechanism of production, nutritional value and its uses in aquaculture nutrition. Aquaculture 531 , 735885 (2021).

Marco, M. L. et al. Health benefits of fermented foods: microbiota and beyond. Curr. Opin. Biotechnol. 44 , 94–102 (2017).

Pan, M. & Barrangou, R. Combining omics technologies with CRISPR-based genome editing to study food microbes. Curr. Opin. Biotechnol. 61 , 198–208 (2020).

Palla, M., Cristani, C., Giovannetti, M. & Agnolucci, M. Identification and characterization of lactic acid bacteria and yeasts of PDO Tuscan bread sourdough by culture dependent and independent methods. Int. J. Food Microbiol. 250 , 19–26 (2017).

Steensels, J., Meersman, E., Snoek, T., Saels, V. & Verstrepen, K. J. Large-scale selection and breeding to generate industrial yeasts with superior aroma production. Appl Environ. Microbiol. 80 , 6965–6975 (2014).

Article   ADS   PubMed Central   PubMed   Google Scholar  

Marullo, P. & Dubourdieu, D. Yeast selection for wine flavor modulation. in Managing Wine Quality (ed. Reynolds, A. G.) 371–426 (Elsevier, 2022). https://www.sciencedirect.com/book/9780081020654/managing-wine-quality .

Tamang, J. P., Shin, D.-H. H., Jung, S.-J. J. & Chae, S.-W. W. Functional properties of microorganisms in fermented foods. Front. Microbiol. 7 , 578 (2016).

Article   PubMed Central   PubMed   Google Scholar  

Sen, T., Barrow, C. J. & Deshmukh, S. K. Microbial pigments in the food industry—challenges and the way forward. Front. Nutr. 6 , 7 (2019).

Wang, Y., Liu, L., Jin, Z. & Zhang, D. Microbial cell factories for green production of vitamins. Front. Bioeng. Biotechnol. 9 , 473 (2021).

Google Scholar  

Yuan, S.-F. F. & Alper, H. S. Metabolic engineering of microbial cell factories for production of nutraceuticals. Micro. Cell Fact. 18 , 1–11 (2019).

Banks, M., Johnson, R., Giver, L., Bryant, G. & Guo, M. Industrial production of microbial protein products. Curr. Opin. Biotechnol. 75 , 102707 (2022).

Jones, S. W., Karpol, A., Friedman, S., Maru, B. T. & Tracy, B. P. Recent advances in single cell protein use as a feed ingredient in aquaculture. Curr. Opin. Biotechnol. 61 , 189–197 (2020).

Shurson, G. C. Yeast and yeast derivatives in feed additives and ingredients: Sources, characteristics, animal responses, and quantification methods. Anim. Feed Sci. Technol. 235 , 60–76 (2018).

Helmy, M., Elhalis, H., Yan, L., Chow, Y. & Selvarajoo, K. Perspective: multi-omics and machine learning help unleash the alternative food potential of microalgae. Adv. Nutr. 14 , 1–11 (2022).

Reyes, T. F., Chen, Y., Fraser, R. Z., Chan, T. & Li, X. Assessment of the potential allergenicity and toxicity of Pichia proteins in a novel leghemoglobin preparation. Regul. Toxicol. Pharmacol. 119 , 104817 (2021).

Xue, Z. et al. Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica . Nat. Biotechnol. 31 , 734–740 (2013).

Yan, J. et al. Engineering Yarrowia lipolytica to simultaneously produce lipase and single cell protein from agro-industrial wastes for feed. Sci. Rep. 8 , 1–10 (2018).

ADS   Google Scholar  

Gleizer, S. et al. Conversion of Escherichia coli to generate all biomass carbon from CO 2 . Cell 179 , 1255–1263.e12 (2019).

Article   CAS   PubMed Central   PubMed   Google Scholar  

Legras, J.-L., Merdinoglu, D., Cornuet, J.-M. & Karst, F. Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol. 16 , 2091–2102 (2007).

Dudley, R. Ethanol, fruit ripening, and the historical origins of human alcoholism in primate frugivory. Integr. Comp. Biol. 44 , 315–323 (2004).

Tamang, J. P. et al. Fermented foods in a global age: East meets West. Compr. Rev. Food Sci. Food Saf. 19 , 184–217 (2020).

Taylor, B. C. et al. Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome. mSystems 5 , e00901–e00919 (2020).

CAS   PubMed Central   PubMed   Google Scholar  

Kim, J. & Adhikari, K. Current trends in kombucha: marketing perspectives and the need for improved sensory research. Beverages 6 , 15 (2020).

He, J., Evans, N. M., Liu, H. & Shao, S. A review of research on plant-based meat alternatives: driving forces, history, manufacturing, and consumer attitudes. Compr. Rev. Food Sci. Food Saf. 19 , 2639–2656 (2020).

Singh, S., Yap, W. S., Ge, X. Y., Min, V. L. X. & Choudhury, D. Cultured meat production fuelled by fermentation. Trends Food Sci. Technol. 120 , 48–58 (2022).

Şanlier, N., Gökcen, B. B. & Sezgin, A. C. Health benefits of fermented foods. Crit. Rev. Food Sci. Nutr. 59 , 506–527 (2017).

Clemente, J. C., Ursell, L. K., Parfrey, L. W. & Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148 , 1258–1270 (2012).

Suez, J., Zmora, N., Segal, E. & Elinav, E. The pros, cons, and many unknowns of probiotics. Nat. Med. 25 , 716–729 (2019).

Wastyk, H. C. et al. Gut-microbiota-targeted diets modulate human immune status. Cell 184 , 4137–4153 (2021).

Bergqvist, S. W., Sandberg, A.-S., Carlsson, N.-G. & Andlid, T. Improved iron solubility in carrot juice fermented by homo-and hetero-fermentative lactic acid bacteria. Food Microbiol. 22 , 53–61 (2005).

Osman, M. A. Changes in sorghum enzyme inhibitors, phytic acid, tannins and in vitro protein digestibility occurring during Khamir (local bread) fermentation. Food Chem. 88 , 129–134 (2004).

Andreasen, A. S. et al. Effects of Lactobacillus acidophilus NCFM on insulin sensitivity and the systemic inflammatory response in human subjects. Br. J. Nutr. 104 , 1831–1838 (2010).

de Angelis, M. et al. Use of sourdough lactobacilli and oat fibre to decrease the glycaemic index of white wheat bread. Br. J. Nutr. 98 , 1196–1205 (2007).

Shetty, P. H. & Jespersen, L. Saccharomyces cerevisiae and lactic acid bacteria as potential mycotoxin decontaminating agents. Trends Food Sci. Technol. 17 , 48–55 (2006).

Nkhata, S. G., Ayua, E., Kamau, E. H. & Shingiro, J.-B. Fermentation and germination improve nutritional value of cereals and legumes through activation of endogenous enzymes. Food Sci. Nutr. 6 , 2446–2458 (2018).

Fang, H. et al. Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B12. Nat. Commun. 9 , 1–12 (2018).

Article   ADS   Google Scholar  

Shen, B. et al. Fermentative production of vitamin E tocotrienols in Saccharomyces cerevisiae under cold-shock-triggered temperature control. Nat. Commun. 11 , 1–14 (2020).

Maintz, L. & Novak, N. Histamine and histamine intolerance. Am. J. Clin. Nutr. 85 , 1185–1196 (2007).

Barbieri, F., Montanari, C., Gardini, F. & Tabanelli, G. Biogenic amine production by lactic acid bacteria: a review. Foods 8 , 17 (2019).

Li, B. & Lu, S. The importance of amine-degrading enzymes on the biogenic amine degradation in fermented foods: a review. Process Biochem. 99 , 331–339 (2020).

Marco, M. L. et al. The international scientific association for probiotics and prebiotics (ISAPP) consensus statement on fermented foods. Nat. Rev. Gastroenterol. Hepatol. 18 , 196–208 (2021).

Jach, M. E., Serefko, A., Ziaja, M. & Kieliszek, M. Yeast protein as an easily accessible food source. Metabolites 12 , 63 (2022).

Yamada, E. A. & Sgarbieri, V. C. Yeast ( Saccharomyces cerevisiae ) protein concentrate: preparation, chemical composition, and nutritional and functional properties. J. Agric Food Chem. 53 , 3931–3936 (2005).

Moreira, J. B. et al. Microalgae polysaccharides: an alternative source for food production and sustainable agriculture. Polysaccharides 3 , 441–457 (2022).

McFarlin, B. K., Carpenter, K. C., Davidson, T. & McFarlin, M. A. Baker’s yeast beta glucan supplementation increases salivary iga and decreases cold/flu symptomatic days after intense exercise. J. Diet. 10 , 171–183 (2013).

Cuskin, F. et al. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 517 , 165–169 (2015).

Article   ADS   CAS   PubMed Central   PubMed   Google Scholar  

Ratledge, C. Fatty acid biosynthesis in microorganisms being used for single cell oil production. Biochimie 86 , 807–815 (2004).

Ritala, A., Häkkinen, S. T., Toivari, M. & Wiebe, M. G. Single cell protein—state-of-the-art, industrial landscape and patents 2001–2016. Front. Microbiol. 8 , 2009 (2017).

Arendt, E. K., Moroni, A. & Zannini, E. Medical nutrition therapy: use of sourdough lactic acid bacteria as a cell factory for delivering functional biomolecules and food ingredients in gluten free bread. Micro. Cell Fact. 10 , 1–9 (2011).

Waters, D. M., Mauch, A., Coffey, A., Arendt, E. K. & Zannini, E. Lactic acid bacteria as a cell factory for the delivery of functional biomolecules and ingredients in cereal-based beverages: a review. Crit. Rev. Food Sci. Nutr. 55 , 503–520 (2015).

Leroy, F. & de Vuyst, L. Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends Food Sci. Technol. 15 , 67–78 (2004).

Denby, C. M. et al. Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer. Nat. Commun. 9 , 1–10 (2018).

Ledesma-Amaro, R. & Nicaud, J. M. Metabolic engineering for expanding the substrate range of Yarrowia lipolytica . Trends Biotechnol. 34 , 798–809 (2016).

Malav, A., Meena, S., Sharma, M., Sharma, M. & Dube, P. A critical review on single cell protein production using different substrates. Int. J. Dev. Res. 7 , 16682–16687 (2017).

Abram, F. Systems-based approaches to unravel multi-species microbial community functioning. Comput Struct. Biotechnol. J. 13 , 24–32 (2015).

Sabra, W., Dietz, D., Tjahjasari, D. & Zeng, A. P. Biosystems analysis and engineering of microbial consortia for industrial biotechnology. Eng. Life Sci. 10 , 407–421 (2010).

McCarty, N. & Ledesma-Amaro, R. Synthetic biology tools to engineer microbial communities for biotechnology. Trends Biotechnol. 37 , 181–197 (2019).

Det-Udom, R. et al. Towards semi-synthetic microbial communities: enhancing soy sauce fermentation properties in B. subtilis co-cultures. Micro. Cell Fact. 18 , 1–8 (2019).

Li, J. et al. Cooperation of lactic acid bacteria regulated by the AI-2/LuxS system involve in the biopreservation of refrigerated shrimp. Food Res. Int. 120 , 679–687 (2019).

Jenkins, G. in SCP—The BP Protein Process. Resources and Applications of Biotechnology (ed. Greenshields, R.) 141–149 (Springer, 1988). https://link.springer.com/book/10.1007/978-1-349-09574-2 .

Hamdan, I. & Senez, J. Protein (SCP) production in the twenty-first century. in Biotechnology: Economic and Social Aspects: Issues for Developing Countries . (eds DaSilva, E. J. & Ratledge, C.) 142–164 (Cambridge University Press, 1992). https://www.cambridge.org/core/books/biotechnology-economic-and-social-aspects/1EE6FBE4E3C1028E2CF7D0C47640D7BD .

Ritala, A., Häkkinen, S. T., Toivari, M. & Wiebe, M. G. Single cell protein-state-of-the-art, industrial landscape and patents 2001-2016. Front. Microbiol. 8 , 2009 (2017).

Finnigan, T. J. A. et al. Mycoprotein: the future of nutritious nonmeat protein, a symposium review. Curr. Dev. Nutr. 3 , nzz021 (2019).

Janssen, M., Wijffels, R. H. & Barbosa, M. J. Microalgae based production of single-cell protein. Curr. Opin. Biotechnol. 75 , 102705 (2022).

Balagurunathan, B., Ling, H., Choi, W. J. & Chang, M. W. Potential use of microbial engineering in single-cell protein production. Curr. Opin. Biotechnol. 76 , 102740 (2022).

Zha, X. et al. Bioconversion of wastewater to single cell protein by methanotrophic bacteria. Bioresour. Technol. 320 , 124351 (2021).

Whittaker, J. A., Johnson, R. I., Finnigan, T. J. A. A., Avery, S. V. & Dyer, P. S. The biotechnology of quorn mycoprotein: past, present and future challenges. in Grand Challenges in Fungal Biotechnology (ed. Nevalainen, H.) 59–79 (Springer, 2020).

Vegetarian & Vegan Products, Meat Free Recipes & News | Quorn. https://www.quorn.co.uk/ .

Zhao, X. R., Choi, K. R. & Lee, S. Y. Metabolic engineering of Escherichia coli for secretory production of free haem. Nat. Catal. 1 , 720–728 (2018). 2018 1:9.

Nokelainen, M. et al. High-level production of human type I collagen in the yeast Pichia pastoris . Yeast 18 , 797–806 (2001).

Williams, K. E. & Olsen, D. R. Gelatin expression from an engineered Saccharomyces cerevisiae CUP1 promoter in Pichia pastoris . Yeast 38 , 382–387 (2021).

Ledesma-Amaro, R. Microbial oils: a customizable feedstock through metabolic engineering. Eur. J. Lipid Sci. Technol. 117 , 141–144 (2015).

Duale, A., Singh, P. & Al Khodor, S. Breast milk: a meal worth having. Front Nutr. 8 , 800927 (2022).

Lu, M., Mosleh, I. & Abbaspourrad, A. Engineered microbial routes for human milk oligosaccharides synthesis. ACS Synth. Biol. 10 , 923–938 (2021).

Bhutada, G. et al. Production of human milk fat substitute by engineered strains of Yarrowia lipolytica . Metab. Eng. Commun. 14 , e00192 (2022).

Braegger, C. et al. Supplementation of infant formula with probiotics and/or prebiotics: a systematic review and comment by the ESPGHAN committee on nutrition. J. Pediatr. Gastroenterol. Nutr. 52 , 238–250 (2011).

Rupa, P. & Mine, Y. Structural and immunological characterization of recombinant ovomucoid expressed in Escherichia coli . Biotechnol. Lett. 25 , 427–433 (2003).

Upadhyay, V., Singh, A. & Panda, A. K. Purification of recombinant ovalbumin from inclusion bodies of Escherichia coli . Protein Expr. Purif. 117 , 52–58 (2016).

Järviö, N. et al. Ovalbumin production using Trichoderma reesei culture and low-carbon energy could mitigate the environmental impacts of chicken-egg-derived ovalbumin. Nat. Food 2 , 1005–1013 (2021). 2022 2:12.

Aro, N. et al. Production of bovine beta-lactoglobulin and hen egg ovalbumin by Trichoderma reesei using precision fermentation technology and testing of their techno-functional properties. Food Res. Int. 163 , 112131 (2023).

Dunn-Coleman, N. S. et al. Commercial levels of chymosin production by Aspergillus. BioTechnology 9 , 976–981 (1991).

Giec, A. & Skupin, J. Single cell protein as food and feed. Food/Nahr. 32 , 219–229 (1988).

Kim, S. W. et al. Meeting global feed protein demand: challenge, opportunity, and strategy. Annu. Rev. Anim. Biosci. 7 , 221–243 (2019).

Chaucheyras-Durand, F. & Durand, H. Probiotics in animal nutrition and health. Benef. Microbes 1 , 3–9 (2010).

Rollo, A. et al. Live microbial feed supplement in aquaculture for improvement of stress tolerance. Fish. Physiol. Biochem 32 , 167–177 (2006).

Dawson, K. A., Newman, K. E. & Boling, J. A. Effects of microbial supplements containing yeast and lactobacilli on roughage-fed ruminal microbial activities. J. Anim. Sci. 68 , 3392–3398 (1990).

Balabanova, L. et al. Engineered fungus Thermothelomyces thermophilus producing plant storage proteins. J. Fungi 8 , 119 (2022).

Xie, D., Jackson, E. N. & Zhu, Q. Sustainable source of omega-3 eicosapentaenoic acid from metabolically engineered Yarrowia lipolytica : from fundamental research to commercial production. Appl. Microbiol. Biotechnol. 99 , 1599–1610 (2015).

Revuelta, J. L. et al. Bioproduction of riboflavin: a bright yellow history. J. Ind. Microbiol. Biotechnol. 44 , 659–665 (2017).

Hanlon, P. & Sewalt, V. GEMs: genetically engineered microorganisms and the regulatory oversight of their uses in modern food production. Crit. Rev. Food Sci. Nutr. 61 , 959–970 (2020).

Ledesma-Amaro, R., Jiménez, A., Santos, M. A. & Revuelta, J. L. Biotechnological production of feed nucleotides by microbial strain improvement. Process Biochem. 48 , 1263–1270 (2013).

Moon, H.-J., Jeya, M., Kim, I.-W. & Lee, J.-K. Biotechnological production of erythritol and its applications. Appl. Microbiol. Biotechnol. 86 , 1017–1025 (2010).

Mohamad, N. L., Mustapa Kamal, S. M. & Mokhtar, M. N. Xylitol biological production: a review of recent studies. Food Rev. Int. 31 , 74–89 (2015).

Xu, Y. et al. De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts. Nat. Commun. 13 , 1–12 (2022).

ADS   CAS   Google Scholar  

Celińska, E. et al. Genetic engineering of Ehrlich pathway modulates production of higher alcohols in engineered Yarrowia lipolytica . FEMS Yeast Res. 19 , foy122 (2019).

Li, J. et al. Simultaneous improvement of limonene production and tolerance in Yarrowia lipolytica through tolerance engineering and evolutionary engineering. ACS Synth. Biol. 10 , 884–896 (2021).

Toogood, H. S. et al. Enzymatic menthol production: one-pot approach using engineered Escherichia coli . ACS Synth. Biol. 4 , 1112–1123 (2015).

Ledesma-Amaro, R. & Nicaud, J.-M. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids. Prog. Lipid Res. 61 , 40–50 (2016).

de Oliveira, E. P. & Burini, R. C. High plasma uric acid concentration: causes and consequences. Diabetol. Metab. Syndr. 4 , 1–7 (2012).

O’Donnell, K., Cigelnik, E. & Casper, H. H. Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the quorn mycoprotein fungus as Fusarium venenatum . Fungal Genet. Biol. 23 , 57–67 (1998).

Nasseri, A. T., Rasoul-Amini, S., Morowvat, M. H. & Ghasemi, Y. Single cell protein: production and process. Am. J. Food Technol. 6 , 103–116 (2011).

Hansen, E. H. et al. De novo biosynthesis of vanillin in fission yeast ( Schizosaccharomyces pombe ) and baker’s yeast ( Saccharomyces cerevisiae ). Appl. Environ. Microbiol. 75 , 2765–2774 (2009).

Kovac, J., den Bakker, H., Carroll, L. M. & Wiedmann, M. Precision food safety: a systems approach to food safety facilitated by genomics tools. TrAC Trends Anal. Chem. 96 , 52–61 (2017).

Liu, W. et al. A dual-plasmid CRISPR/Cas system for mycotoxin elimination in polykaryotic industrial fungi. ACS Synth. Biol. 9 , 2087–2095 (2020).

Grasso, A. C., Hung, Y., Olthof, M. R., Verbeke, W. & Brouwer, I. A. Older consumers’ readiness to accept alternative, more sustainable protein sources in the European Union. Nutrients 11 , 1904 (2019).

Onwezen, M. C., Bouwman, E. P., Reinders, M. J. & Dagevos, H. A systematic review on consumer acceptance of alternative proteins: pulses, algae, insects, plant-based meat alternatives, and cultured meat. Appetite 159 , 105058 (2021).

Sultana, S., Ali, M. E. & Ahamad, M. N. U. Gelatine, collagen, and single cell proteins as a natural and newly emerging food ingredients. in Preparation and Processing of Religious and Cultural Foods (eds Ali, E., Naquiah, N. & Nizar, A.) 215–239 (Elsevier, 2018).

Voutilainen, E., Pihlajaniemi, V. & Parviainen, T. Economic comparison of food protein production with single-cell organisms from lignocellulose side-streams. Bioresour. Technol. Rep. 14 , 100683 (2021).

Jach, M. E. et al. Statistical evaluation of growth parameters in biofuel waste as a culture medium for improved production of single cell protein and amino acids by Yarrowia lipolytica . AMB Express 10 , 1–12 (2020).

Linder, T. Edible microorganisms—an overlooked technology option to counteract agricultural expansion. Front. Sustain Food Syst. 3 , 32 (2019).

Menezes, A. A., Montague, M. G., Cumbers, J., Hogan, J. A. & Arkin, A. P. Grand challenges in space synthetic biology. J. R. Soc. Interface 12 , 20150803 (2015).

García Martínez, J. B. et al. Potential of microbial protein from hydrogen for preventing mass starvation in catastrophic scenarios. Sustain Prod. Consum. 25 , 234–247 (2021).

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R.L.-A. received funding from BBSRC (BB/R01602X/1, BB/T013176/1, BB/T011408/1–19-ERACoBioTech- 33 SyCoLim), British Council 527429894, Newton Advanced Fellowship (NAF\R1\201187), Yeast4Bio Cost Action 18229, European Research Council (ERC) (DEUSBIO–949080) and the Bio-based Industries Joint (PERFECOAT- 101022370) under the European Union’s Horizon 2020 research and innovation programme.

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Fermentation has been used for thousands of years to produce various foods and beverages. In recent decades, research has been increasingly devoted to studying the microbiome of fermented food and beverages, unraveling the main aspects of the ecology of bacteria, fungi, and yeasts, and their impacts on ...

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An overview of fermentation in the food industry - looking back from a new perspective

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Fermentation is thought to be born in the Fertile Crescent, and since then, almost every culture has integrated fermented foods into their dietary habits. Originally used to preserve foods, fermentation is now applied to improve their physicochemical, sensory, nutritional, and safety attributes. Fermented dairy, alcoholic beverages like wine and beer, fermented vegetables, fruits, and meats are all highly valuable due to their increased storage stability, reduced risk of food poisoning, and enhanced flavor. Over the years, scientific research has associated the consumption of fermented products with improved health status. The fermentation process helps to break down compounds into more easily digestible forms. It also helps to reduce the amount of toxins and pathogens in food. Additionally, fermented foods contain probiotics, which are beneficial bacteria that help the body to digest food and absorb nutrients. In today’s world, non-communicable diseases such as cardiovascular disease, type 2 diabetes, cancer, and allergies have increased. In this regard, scientific investigations have demonstrated that shifting to a diet that contains fermented foods can reduce the risk of non-communicable diseases. Moreover, in the last decade, there has been a growing interest in fermentation technology to valorize food waste into valuable by-products. Fermentation of various food wastes has resulted in the successful production of valuable by-products, including enzymes, pigments, and biofuels.

Introduction

The growing concern about the availability of safe and sustainable natural food supplies is a direct result of a rapidly expanding global population (Knorr and Augustin 2022 ). For the production of the next generation of food components and products, fermentation stands out among other approaches like cellular or acellular products, edible biomass, and edible insects. Compared to conventional farming, the production of fermented products requires reduced land, generates fewer greenhouse gas emissions, and consumes less water. Additionally, fermented foods have been linked with health benefits such as lowering cholesterol levels, boosting the immune system, protecting against infections, cancer, osteoporosis, obesity, diabetes, allergies, atherosclerosis, and reducing lactose sensitivity (Tamang and Thapa 2022 ). The beneficial effects of fermented foods are mostly credited to bioactive peptide fractions produced during fermentation through microbial protein breakdown (Şanlier et al. 2019 ).

Fermentation is a time-honored method used for ages to prolong the shelf life of food and augment its nutritional quality (Augustin et al. 2023 ). It has been used to preserve various animal-derived, seafood, and plant-originated foods. Middle Eastern, European, and Indian cultures developed cheese, cultured milk, and fermentation-based milk products. On the contrary, animal husbandry was more restricted to Eastern countries including Japan, Korea, and China. A wide range of ingredients used to produce alcoholic beverages and fermented foods was also influenced by cultural, social, religious, and economic variables. Therefore, fermented foods that originated in Asia tended to be based on rice and grains, vegetables, fish, and soybeans, while in Africa, native cereal grains such as millet, sorghum, maize, and wheat represent popular fermenting substrates (Tamang et al. 2020 ). The regulated action of microorganisms on a food substrate is at the root of fermentation. Fermentation may be spontaneously induced by microorganisms commonly found in raw ingredients. Traditional sauerkraut, sourdough bread, and kimchi result from fermented foods rendered through spontaneous fermentation. Advances in biotechnology have made fermentation into an established process. Using starting cultures allow for acquiring a standardized food product (Bourdichon et al. 2021 ). For food applications, strain engineering often involves harmless microorganisms like  Bacillus spp., yeast like  Saccharomyces cerevisiae ,  Komagataella phaffii ,  Kluyveromyces spp., or filamentous fungi (Augustin et al. 2023 ; Chai et al. 2022a , b ; Vieira Gomes et al. 2018 ). Specific food components like antioxidants, colorants, flavors, enzymes, and vitamins can also be manufactured through fermentation (Santiago‐Díaz et al. 2022 ). Antioxidants, bacteriocins, pigments, enzymes, and other food components are increasingly being manufactured utilizing food waste as a fermentation substrate. A direct connection exists between eliminating food waste and developing creative, high-value assets generated by applying an under- or untapped resource (Yang et al. 2022 ). In the bargain, scientific investigations have ensured insights into using fermentation technology to produce fermented edible insects to promote food security. There are already available fermented insect-containing edible preparations such as sauces, powder, paste, and fermented dishes containing insects with the possibility of extension (Kewuyemi et al. 2020 ). Examples of such fermented sauces include those made using Locusta migratoria and Galleria mellonella . These sauces were very satisfactory compared with conventional seafood sauces (Mouritsen et al. 2017 ).

Fermentation further improves compound extraction efficiency, alters the antioxidant profile, and generates novel bioactive compounds from the food matrix. Lately, there is an emerging understanding that precision fermentation represents a key innovation in the food industry’s impending fourth industrial revolution. Modernizing food production with precision fermentation is becoming increasingly popular. Because of its potential to reduce waste and increase the efficiency of protein, lipid, and carbohydrate production (Augustin et al. 2023 ). This overview will discuss fermentation’s cultural significance and ecological importance, technological advancements of fermented beverage and food worldwide, health benefits, nutritional value, and microbiological insights into various fermented foods. We will examine distinct types of fermented foods of animal, plant, microalgae, and edible insect origin. For every kind of product, bacteria involved in fermentation, consumers’ acceptance, place of origin, and consumption will be discussed. There is also a discussion of how the industrial revolution has impacted the process of fermented foods and how fermentation is used to value food waste.

Technology advancements in fermentation

The process of fermentation encompasses the biochemical activity of organisms throughout their life cycle, from growth to death. Industrial-scale production of food, pharmaceuticals, and alcoholic beverages utilizes fermentation technology powered by these organisms. Industrial fermentation technology relies on the fundamental principle of cultivating organisms in optimal conditions. This is achieved by providing the required raw materials, including carbon, nitrogen, salts, trace elements, and vitamins, essential for their growth (Sharma et al. 2020 ). Additionally, the temperature, pH, and oxygen concentrations must be controlled in order to ensure the highest possible yield of the desired product. The fermentation process is also closely monitored to ensure that the organisms are not exposed to any toxins or pathogens that could potentially affect the outcome. The mounting focus on environmental conservation and renewable energy has sparked a surge of interest in the retrieval of fermentation products, including industrial chemicals, organic acids, and feed or food additives. This upswing has caused a proliferation of products beyond the customary high-value, low-volume pharmaceuticals, with fermentation now rivaling the synthesis of commodity chemicals itself. Companies must optimize efficiency and reduce waste by-products to remain competitive in producing low-cost, high-volume chemicals. Currently, scientific communities are keenly exploring the biotechnological potential of agro-industrial remnants.

Emerging fermentation-based technologies have revolutionized the food industry in various ways. Cai et al. ( 2020 ) reported that sulforaphane yields were increased by 16 times when broccoli florets were pre-heated at 65 °C for 3 min followed by maceration and lactic acid bacteria fermentation in a laboratory scale. Additionally, these technologies have paved the way for producing a pea protein hydrolysate component that enhances the saltiness of food. In a study by Xu et al. ( 2020 ), fermentation of carrot juice was found to enhance the nutritional profile of carrot juice by using probiotic Lactobacillus gasseri . Fermented straight carrot juice was found to have a reduction in sugar (27%) according to their results. It is possible to improve fermentation processes and tweak fermented foods’ nutritional and sensory attributes using these methods. To enhance fermentation, the following factors at each stage need to be addressed: selecting and designing of targets, strain optimization, bioprocess development, feedstock improvement, and final product formulation and production. One fermentation technique utilized by various industries, including food, pharmaceuticals, and textiles, is solid-state fermentation (SSF), which involves utilizing solid support rather than a liquid to produce microorganism metabolites. SSF boasts several benefits: minimal waste production and a reduced environmental impact, natural solids as a medium with low energy costs and capital investments, no sterilization requirement, improved downstream processes and reduced microbial contaminants (Sun et al. 2022 ).

Acidogenic fermentation (AF) is crucial in producing valuable chemicals like C1–C6 carboxylic acids and alcohol. However, low product titers have been a persistent challenge due to thermodynamic limitations. Recent research shows that boosting the redox potential in AF can enhance metabolic pathways, enabling a smoother flow of electrons and lowering activation energy barriers. This improves substrate utilization rates, product yields, and speciation. This augmented system, known as electro-fermentation (EF), has tremendous potential to revolutionize fermentation technology by offering an exogenous electricity supply (Chandrasekhar and Venkata Mohan 2014 ; Luo et al. 2022 ; Nagarajan et al. 2022 ).

Ultrasound waves that exceed 20 kHz have emerged as an eco-friendly option for processing agri-foods. This sound technology applies a cavitation process, during the formation of bubbles and their burst, leading to a sterilization effect on food and drink products. Ultrasonication aids in the deactivation of enzymes and microorganisms by disrupting the cell membrane (Gavahian et al. 2022 ). Ultrasonic systems are easily applicable on an industrial scale as they do not require immersion of the product into a liquid medium. This allows hydrophilic nutritional compounds to be maintained, enabling these systems to be employed on a large scale. Wineries have successfully employed this emerging technology to enhance wine aroma, flavor, color, and phenolic profile. Research has uncovered the benefits of ultrasonic technology on wine fermentation and aging. This innovative approach improves wine quality by increasing the key aging indicators including phenolic substances and color intensities and deactivates microbes. Furthermore, ultrasound application results in enhanced physiological, phytochemical, biochemical, and organoleptic characteristics of alcoholic drinks. Celotti et al. ( 2020 ) investigated the influence of high power ultrasound on anthocyanins and phenolic levels in red young wines. Following 15 and 30 days of storage, the tannin content of the treated wine decreased by 15% and 40%, respectively, due to the higher ultrasound amplitude (81%). This suggests that high power ultrasound can be used to significantly reduce the tannin content of red young wines, making them less bitter and more palatable. Moreover, Zhang et al. ( 2016 ) studied the physicochemical characteristics of red wine after ultrasound treatment. 240 W of power ultrasound, a frequency of 80 kHz, and a temperature of 20 °C are considered optimal conditions for ultrasound application in red wine processing. A significant change was observed in total phenolic compounds, electrical conductivity, and chromatic characteristics of the samples. However, pH or acidity titratable did not differ significantly. These studies provide evidence that ultrasound treatment can be used as an effective tool to manipulate the physicochemical characteristics of red wine.

The benefits of producing lactic acid from renewable sources have sparked much interest across different fields. The petrochemical industry has embraced this approach for its high yield and cost-effective productivity using readily available substrates (Zhao et al. 2016 ). However, the disposal of biomass and waste materials from various sources poses a significant environmental challenge (RedCorn and Engelberth 2016 ). The ideal solution is an integrated biorefinery platform that produces high-value bioproducts while addressing waste management. The potential applications of fermentation-produced optical pure lactic acid in the food, pharmaceutical, cosmetic, and the textile industry have made it a highly promising option for packaging materials. Polylactic acid, derived from natural resources, is a green substitute for petrochemical-based bioplastics. While biodegradability is a significant advantage, lactic acid's high price production has hindered the widespread application of this material (Bastidas-Oyanedel et al. 2015 ; Kumar et al. 2019 ).

In developing countries, small-scale food fermentation technologies have been refined through practical wisdom rather than scientific innovation. As a result, many manufacturers need more certainty about modernizing and altering their fermentation processes. However, it is crucial to enhance the safety and quality of fermented foods while preserving their distinctiveness and keeping production costs low. One practical approach is the consortium method, which has successfully improved Thailand's small-scale soy sauce fermentation (O’toole 2019 ). This approach facilitates ongoing collaboration between industry and scientists, providing the latter with the necessary research focus to help the industry thrive. While the small-scale fermentation industry has hesitated to embrace starter cultures due to concerns over the loss of unique flavor, modern molecular biology techniques have ushered in a new era of tailored starter culture development. In recent studies, microflora from distinct product origins exhibited variations in sensory quality and composition, highlighting the potential for customization. To support this trend, a cell bank is currently in the works as a resource for Thai fermented pork sausage, intending to ease the implementation of starter cultures in production (Østergaard et al. 1998 ; Mongkolwai et al. 1997 ; Valyasevi and Rolle 2002 ).

Fermentation in the food industry as an environmentally friendly alternative to improve nutritional value

Global population growth often correlates with increased demand for food and energy. Large amounts of food waste have been generated by industrialization and lack of proper waste management strategies (Ng et al. 2020 ). By 2030, 2.1 billion tons of food waste will be generated annually, according to a Boston Consulting Group report (Martin-Rios et al. 2021 ). The agricultural and food processing industries face two major challenges. On the one hand, it is critical to limit their impact on the environment to minimize climate change effects. Conversely, the insufficiency of superior alternatives to health-promoting diets (Rastogi et al. 2022 ). Food shortages and environmental consequences result from lost and wasted agricultural output during processing and distribution (Read et al. 2020 ). A high proportion of nutrients are found in plant-based food processing waste, including pulp, peels, and silage, but these materials are typically disposed of in landfills or washed into water bodies, causing the fast depletion of dissolved oxygen (Ishangulyyev et al. 2019 ). A high sugar, refined carb, processed meat, artificial additive, and trans-fat diet is also linked to obesity, Type 2 diabetes (T2D), hormonal imbalances, and cardiovascular disease (Tandon et al. 2022 ). Food fermentation technology has a number of advantages, including environmental and health benefits (Paramithiotis et al. 2022 ; Rastogi et al. 2022 ). In fermented foods, microorganisms and enzymes are involved in the enzymatic transformation of food substances, emphasizing microbial changes as the distinguishing feature.

A wide range of fermented products make up FFs, including fermented meat, fish, dairy products, fermented fruits, and alcoholic drinks. Furthermore, they include vinegar, cocoa, soy sauce, fish sauce, and coffee (Gänzle 2022 ). Industrial FF production has evolved from household techniques. Fermented beverages are uncontrolled at household levels due to ubiquitous microorganisms. Traditional fermentation, despite being economical, also preserves food (Adesulu and Awojobi 2014 ). A functional microorganism provides the health benefits of antibacterial, antioxidant, and peptide synthesis in FFs. Additionally, fermentation can produce nutritious foods and sustainable food supplies. Compared to traditional chemical synthesis methods, fermentation is more flexible, cost-effective, and environmentally friendly (Fig.  1 ). There has been more investigation into fermentation-based synthesis, optimization, and downstream of medicines, biofuels, biofertilizers, and biodegradable polymers (Rastogi et al. 2022 ). Microbiological fermentation converts green waste into valuable products. Food waste is considered edible or inedible fractions originating from animals or plants generated before or after consumption (Torres-León et al. 2021 ). Fermentation technique for bioconversion is significantly influenced by the type of food waste used. Solid-state fermentation is often performed on solid substrates to improve nutrient efficiency, while submerged fermentation is generally used on liquid substrates (Sadh et al. 2018 ). Due to its low cost, high productivity, and simplicity, submerged fermentation is more commonly used in industrial-scale fermentation. Food waste is considered an excellent input for microbial fermentation due to its abundance of phenolics, proteins, fatty acids, minerals, and several bioactive ingredients. Therefore, the biotransformation of these rich sources allows value-added outputs without waste treatment (Dursun and Dalgıç, 2016 ; Ng et al. 2020 ). Food processing wastes can be used to produce enzymes, biofuels, oligosaccharides, growth-promoting agents, polysaccharides, bioplastics, proteins, and bioactive compounds (Sadh et al. 2018 ; Torres-León et al. 2021 ).

Fermentation’s primary benefits. “Created with BioRender.com”

Lipids extracted from waste materials can also be precursors to bioethanol synthesis (96%) through fermentation (Ashokkumar et al. 2022 ). Reducing waste, increasing energy production, and developing other healthcare products are all enhanced by transforming organic waste into value-added bioproducts. Bioproducts such as protease enzyme have been produced by microbial fermentation of food waste (De Castro et al. 2015 ; Mathias et al. 2017 ), β-glucosidase enzyme using brewer´s spent grain (BSG) as substrate (Leite et al. 2019 ), antioxidant peptides using microorganism fermentation ( Aspergillus oryzae ) and turbot skin as substrate (Fang et al. 2017 ). Sepúlveda et al. ( 2020 ) conducted a study to develop ellagic acid using polyphenols from orange peel wastes through submerged fermentation. This study demonstrated the effectiveness of this method for converting molecules present in orange waste to produce high-value products like ellagic acid. A combined submerged and solid-state fermentation method using Neurospora intermedia was successfully used by Gmoser et al. ( 2019 ) for the conversion of waste bread into protein and carotenoids. By using wheat waste as a substrate, Dursun and Dalgıç ( 2016 ) achieved astaxanthin pigment production by four different yeast species. It is difficult to estimate the bioproducts produced through bioconversion processes due to the unidentified exact amounts of bioactive content of food waste. Thus, innovative biotechnology techniques must be employed to optimize the reutilization and recycling of food-processing and agricultural wastes (Ng et al. 2020 ).

Consumers' desire for healthier foods drives manufacturers to seek out new methods of preparing food (Adebo et al. 2018 ). While FFs were initially developed to prolong foods’ shelf-life, they are now commonly used to enhance food safety, sensory quality, and nutritional value (Macori and Cotter 2018 ). Lately, there has been a surge in awareness of FFs as possible sources of functional foods (Adebo et al. 2018 ). The fermentation process alters substrates and generates biologically active or biologically available final products, improving nutritional and functional properties. Fermentation by-products such as organic acids, ethanol, and bacteriocins minimize contamination risk (Marco et al. 2017 ). Beneficial microorganisms, or derivatives obtained from fermentation may contribute to the health benefits of FF consumption (Adebo et al. 2018 ; Macori and Cotter 2018 ; Marco et al. 2017 ).

Fermentation changes the nutritional and bioactive qualities of food matrices. This is due to the combined effects of the raw material's enzymatic activity and microorganism metabolism (Savaiano 2014 ). In plant-based fermented foods, lactic acid bacteria produce glycosyl hydrolase, esterase, decarboxylase, and phenolic acid reductase to convert phenolic substances into physiologically active metabolites (Filannino et al. 2015 ). The fermented dairy products contain biologically active peptides such as yogurt, cheese, fermented milk, kefir, dahi, etc. These peptides have anti-thrombotic, anti-hypertensive, immune-modulatory, osteogenic, and antioxidant properties. LABs generate biological peptides by breaking down dairy proteins (Pihlanto and Korhonen 2015 ). Fermentation metabolites vary by strain, but lactic acid (LA) is the primary product. Lactic acid can reach 1% in several LAB fermentations. Pro-inflammatory cytokines, bone marrow-derived macrophages, and dendritic cells are diminished by LA in a dose-dependent manner (Iraporda et al. 2015 ; Marco et al. 2017 ). Despite the enhanced availability of trace minerals and vitamins, fermentation of plant and dairy matrices amplifies the production of vitamins, particularly folate, riboflavin, and B12 (Macori and Cotter 2018 ; Marco et al. 2017 ). Fermentation quality depends strongly on the activity of the microorganisms involved in the process and the substrate used in fermentation. As prebiotics, fibers enhance fermentation bacteria's microbial population, while also influencing the biochemical profile of the final products with health benefits (Adebo et al. 2018 ). Intestinal health can be positively impacted by short-chain fatty acids including butyric acid, propionic acid, and acetic acid derived from dietary fiber fermentation (Hati et al. 2019 ; Kang et al. 2021 ). Fermentates may also provide some health benefits of FFs. A fermentate is a powdered preparation incorporating beneficial bacteria, metabolites, and bioactive components derived from fermentation and substrates (Mathur et al. 2020 ). A range of fermentates containing different ingredients have been shown to have beneficial outcomes, including effects on gut health due to the production of lactose-hydrolyzed products for lactose intolerant individuals and the production of glycosylated products using β -galactosidases enzyme (Saqib et al. 2017 ), regulates food intake and prevents weight loss using glucagon-like peptide-1 (GLP-1) (Cho et al. 2014 ; van Bloemendaal et al. 2014 ), the anti-inflammatory activity of paraprobiotic CP2305 ( Lactobacillus gasseri CP2305) by affecting the growth of fecal Bacteroides vulgatus and Dorea longicatena , which are involved in intestinal infection (Nishida et al. 2017 ), as well as the potential benefits of heat-killed bacteria in treating dermatological disorders (Piqué et al. 2019 ). Heat-killed Lactobacillus kunkeei YB38 increased bowel movements and improved the intestinal environment in humans, according to Asama et al. ( 2016 ). Warda et al. ( 2019 ) found that long-term intake of an ADR-159 diet containing inactivated lactobacilli had no negative effects on health outcomes of male mice.

Fermented foods and non-communicable diseases

Dietary habits are significant in the hierarchy of essential factors triggering non-communicable diseases (NCD). High saturated fatty acids, sodium, a sedentary lifestyle, and a diet poor in fruits and vegetables are some risk factors for developing NCD (Angeles-Agdeppa et al. 2020 ). From a health stance, integrating FFs into the daily diet has been in the spotlight of several investigations. The presence of beneficial microorganisms such as LABs concomitantly with their biologically active metabolites has been associated with several positive effects concerning NCD (Mathur et al. 2020 ). LAB fermentation technologies provide various bioactive substances with potential health benefits (Mathur et al. 2020 ).

The health benefits generated from fermented products are mainly regarded as the metabolic activities of the fermenting microbial community or their biologically active metabolites (Table 1 ). As an example, various LABs have been found to produce exopolysaccharides (EPSs) during fermentation. The produced EPSs have been related to different health benefits, including antidiabetic, cholesterol-reducing, antioxidant, and immunomodulatory effects (Nampoothiri et al. 2017 ; Patel and Prajapat 2013 ). EPSs derived from LABs exhibit their anti-cholesterol activity by alleviating cholesterol assimilation in the intestine and inducing the release of bile acids (Nampoothiri et al. 2017 ). Among FFs, fermented dairy products have been linked to a variety of health benefits. Dairy products represent a rich source of proteins, fat, and lactose which generate different bioactive molecules due to their enzymatic activities. During fermentation, several different LAB strains may secrete enzymes that help break down complicated inedible substrates into more easily digestible ones. These enzymes include β-galactosidase, amylase, protease, lipase, and glucoamylase (Macori and Cotter 2018 ; Marco et al. 2017 ). The secretion of the β-galactosidase enzyme facilitates the breakdown of lactose, thus addressing lactose intolerance. Despite facilitating nutrient absorption, particularly in fermented cereals, LABs contribute to removing toxic compounds such as phytic acid by enhancing phytase activity (Marco et al. 2017 ).

Intake of fermented dairy was correlated with a lower incidence of cardiovascular diseases. Furthermore, additional research quantifying the functional impact and side effects may give a more understandable mechanism (Zhang et al. 2020a ). Moreover, anti-hypertensive angiotensin-converting-enzyme (ACE) inhibitor peptides in fermented dairy products are particularly interesting (Fekete et al. 2015 ). The anti-hypertensive effect is also induced by several bioactive compounds in fermented dairy, including valyl-prolyl-proline and isoleucyl-prolyl-proline (Nongonierma and FitzGerald 2015 ). Among NCDs, cancer has been regarded as one of the most critical diseases closely related to dietary habits. It is predicted that 30–40% of cancer cases may be averted by modifying risk factors and behavioral modifications, the most important of which is food. There is evidence that suggests that consuming FFs may lower cancer risk due to the presence of specific nutrients (Tasdemir and Sanlier 2020 ). The occurrence of diverse reactive oxygen species and other free radicals due to various metabolic reactions beyond the tolerance levels disrupts body homeostasis. The presence of disorders at the cellular level advances the appearance of cancer. Antioxidants are assumed to impair carcinogenesis by preventing DNA from free radicals, slowing cell proliferation in response to oxidants, and triggering apoptosis (Khurana et al. 2018 ; Tasdemir and Sanlier 2020 ). Fermentation is finalized by producing specific products with robust antioxidant properties, including phenolic compounds, anthocyanins, EPSs, and bioactive peptides (Kok and Hutkins 2018 ; Marco et al. 2017 ; Tasdemir and Sanlier 2020 ). Gao et al. ( 2013 ) have outlined the anti-tumor effects of bioactive substances generated from FFs on the gastric cancer cell line SGC7901. Conversely, T2D significantly contributes to an individual’s reduced life expectancy (Sivamaruthi et al. 2018 ). Several in vitro, in vivo, and clinical investigations have reported the antidiabetic impacts of FFs. (Fujita et al. 2017 ) have noted that  camu-camu  fermented with LABs can support T2D and hypertension. Furthermore, Raffaelli et al. ( 2015 ) outlined that fermented papaya fruit can mitigate diabetes-related oxidative damage. By increasing membrane permeability, fermented papaya fruit improves platelet function. Fermented  Moringa oleifera  could ameliorate glucose intolerance in high-fat diet obese mice (Joung et al. 2017 ).

Fermented foods have been reported to have an antidiabetic effect in numerous scientific studies. Algonaiman et al. ( 2022 ) investigated the antidiabetic and hypolipidemic properties of fermented oat extract in rats. The study found that the fermented oat extract had a significant effect on blood glucose levels and lipid profile of the rats. It also improved body weight and decreased oxidative stress in the rats. The results suggest that fermented oat extract may be a potential alternative for the management of diabetes. The antidiabetic properties of lactic acid bacteria isolated from traditional fermented foods were evaluated by Cai et al. ( 2019 ). The results showed that the lactic acid bacteria were effective in reducing blood glucose levels and had a protective effect against oxidative stress. This suggests that lactic acid bacteria could be used to develop functional food products for the management of diabetes. Two Lactobacillus species were used in the study by Feng et al. ( 2018a , b ) to assess fermented buckwheat's antidiabetic effects. They reported that tartary buckwheat fermented with L. plantarum TK9 and L. paracasei TK1501 has the potential to regulate blood glucose in diabetics. Antidiabetic effects of fermented lettuce extracts were studied by Jeong et al. ( 2021 ). This study indicates fermented lettuce extract could be considered an effective additive to diabetic foods to balance blood glucose levels and improve insulin resistance. The antibacterial and antidiabetic properties of synbiotic fermented milk have been studied by Shafi et al. ( 2019 ). In diabetic rabbits, the product was found to reduce blood glucose levels, urea levels, and creatinine levels. Antioxidant, antimicrobial, and antidiabetic activities of probiotic-fermented blueberry juices were significantly improved compared to non-fermented juices (Zhong et al. 2021 ).

Additionally, bioactive metabolites of fermentation are well-known for their immune-modulatory properties. Consumption of FFs has been associated with increased IgA-producing cells and enhanced macrophage activity (Park and Bae 2016 ). Immunomodulation is related to the generation of cytokines such as IL-12, tumor necrosis factor-gamma (TNF-y), and interferon-y (IFN-y) as a consequence of increased T cell and dendritic cell activity (Jones et al. 2014 ). Irritable bowel syndrome (IBS), for example, may also be controlled with fermented foods like kimchi, Crohn’s disease, and infections caused by external invasions or poor eating habits (Han et al. 2020 ; Kim and Park 2018 ; Seong et al. 2021 ). Glucagon-like peptide-1 (GLP-1) is a significant hormone linked to suppressed appetite, and it has been hypothesized that inducing GLP-1 reduces appetite and food consumption (Cho et al. 2014 ; van Bloemendaal et al. 2014 ). (Chaudhari et al. 2017 ) have reported that fermentates of  Lactobacillus helveticus  induce the proglucagon and secretion of GLP-1 in STC-1 (pGIP/Neo) cells.

Food allergies

Allergy is one of the most severe NCD associated with food intake. Although food-related allergies are estimated to affect 1–10% of the population, the prevalence of the condition is reported to be higher in children, reaching 5–12.6% (Pi et al. 2022 ). Foods like milk, egg, shellfish, peanut, soy, wheat, and fish are most commonly associated with allergies (Ricci et al. 2019 ). Food allergies typically appear within two hours of exposure because there is no immunological and clinical tolerance to the food allergen (Barni et al. 2020 ). Because it is almost impossible to exclude allergens from dietary patterns, processing these items has received greater significance (Fu et al. 2019 ). Physical, chemical, and biological processes may reduce allergens in food. Compared to other existing procedures, fermentation is also convenient and safe, besides improving the physicochemical and nutritional value of the foods (Pi et al. 2019 ). Fermentation alleviates food allergies in several ways. High molecular substances, including proteins, may be broken down through fermentation into more tolerable low molecular entities like small molecule polypeptides and amino acids, causing an alteration in structure and altered characteristics (Fu et al. 2019 ).

A number of pathways occur during fermentation that reduce the allergenicity of food allergens, such as proteolytic enzymes, denaturation by acidic environments, glycosylation, and the Maillard reaction (Pi et al. 2019 ). Several metabolites formed from fermentation can regulate the immune system by adjusting the proliferation and cytokine release from T cells, Th 17 cells, and Treg cells (Dargahi et al. 2019 ). For instance, propionic acid produced from fermentation induces dendritic cells to generate TGF-b and retinoic acid. TGF-b and retinoic acid cause a switch of naive T cells to Tregs and inhibit Th2 generation. Additionally, fermentation metabolites such as 10-hydroxy cis-12-octadecenoic acid and linoleic acid escalate intestinal barrier function and lower systemic food allergen levels (Hirata and Kunisawa 2017 ). Moreover, the soy-derived acidic polysaccharide APS-I has also been shown to stimulate IgA synthesis in the intestines (Cao et al. 2019 ). pH, temperature, and substrate are among the processing parameters in the allergenicity reduction is microbial strain utilized in fermentation. Fermentation's influence on dietary allergies is most visible in some foods, such as peanuts, soybeans, milk, etc. (Fu et al. 2019 ). For instance, allergenicity in fermented cow, buffalo, and goat milk was reduced after co-cultivation of  Lactobacillus helveticus ,  Lactobacillus delbrueckii  subsp.  bulgaricus , and  Streptococcus thermophilus  (Anggraini et al. 2018 ). Likewise, the proteolytic activity of  Enterococcus faecalis  VB63F decreased the allergenicity of fermented bovine milk by degrading the protein fraction (Bos d 9–11) responsible for the allergic reaction (Biscola et al. 2016 ).  Bacillus  spp. has been reported to exhibit anti-allergic effects when used in several plant-based foods' fermentation. For instance, results showed that the allergenicity of peanut protein could be reduced by using  Bacillus natto  in a fermentation process using peanut pulp (Jiang et al. 2020 ). Moreover, according to Yang et al. ( 2020 ),  Bacillus subtilis  showed the most significant hypoallergenic impact (44.5%) in the allergenicity of soybean when compared to other fermenting bacteria. Mecherfi et al. ( 2019 ) reported that  Lactococcus lactis  reduced gluten-related sensitization. The primary epitopes responsible for wheat allergy were found in the gliadin repeating domain hydrolyzed by  L. lactis . Multiple bacterial strains used in fermentation are more effective in alleviating food allergenicity. Nevertheless, it should not be underestimated that some strains can produce bitter peptides that negatively affect the taste of the fermented product. Consequently, fermenting food offers a new approach to lowering the allergenicity of diverse foods when combined with other processing methods, such as heat treatment, pulsed light, and ultrasonication (Pi et al. 2019 ).

Fermentation microbiology

Fermentation is an ancient activity dating back to the earliest human civilizations when scientific principles were not yet recognized and studied (El-Mansi et al. 2019 ). According to the International Scientific Association for Probiotics and Prebiotics (ISSAP), foods that have undergone microbial growth and enzymatic conversion are defined as fermented foods (Marco et al. 2021 ). Fermentation helps to preserve foods, making them last longer and making them easier to digest. It also adds flavor, texture, and nutrition to foods, making them more appealing to consumers. Additionally, fermentation helps to break down complex compounds into simpler forms that can be more easily absorbed by the body. During food fermentation, complex components are broken down into simpler parts, many of which may be biologically active, using microorganisms (Macori and Cotter 2018 ). Available scientific data indicate that many fermented foods contain both nutritive and non-nutritional components that can control particular target processes in vivo related to consumer well-being and health (Tamang et al. 2016 ). The presence of microorganisms in fermented foods can provide consumers with numerous health benefits, such as probiotic properties, antibacterial properties, antioxidant properties, and peptide synthesis (Tamang et al. 2016 ). Therefore, regular consumption of fermented foods may significantly contribute to improved human health.

Fermentation is a widely used process in the food industry, and its products are diverse and beneficial to our health. Different types of fermentation can be categorized based on the microorganisms involved in the fermentation process, the primary metabolites produced by these microorganisms, the raw materials used, the fermentation method, oxygen demand, pH level, and nutritional metabolism (Vilela et al. 2019 ). The most common category, based on the microorganisms responsible for the fermentation and its product, is acetic acid (vinegar), lactic acid (dairy products, vegetables, cereals, meat), ethanol/alcohol (baking, brewing, winemaking), alkaline (Japanese natto) (Vilela et al. 2019 ). Fermentation typically involves the utilization of compounds from the feedstock by microorganisms such as yeast and lactic acid bacteria (LAB) like Lactobacillus, Lactococcus, Pediococcus, Enterococcus, and Streptococcus, commonly found in fermented milk products. These microorganisms produce a variety of compounds, including alcohols, acids, and gases, during the fermentation process. These compounds can be used to produce a variety of products, such as fermented dairy products and alcoholic beverages. As a subfield of bioengineering, fermentation has gained increasing attention from a variety of fields, including microbiology, chemical engineering, genetic engineering, cell engineering, mechanical engineering, software, and computer hardware (Feng et al. 2018b ). There is no doubt that fermentation is a significant field of research and that its potential applications are still expanding. Fermentation can be applied to manufacture pharmaceuticals, chemicals, and biofuels, and produce food, beverages, and animal feed. It is an efficient and cost-effective process, and can also be used to produce renewable energy. Multiple microbe interactions lead to fermented foods, primarily traditional fermented foods. During food fermentation, flavor-active compounds form due to proteolysis and hydrolysis of peptides, with the conversion of amino acids and the formation of flavor-enhancing amino acid compounds (Zhao et al. 2016 ). Many fermented filtrates or extracts have potential health benefits, including high nutritional value, antioxidant activity, gut microbiome balance, and immune enhancement (Kim et al. 2019 ). Highly selective biocatalytic processes regulate complex systems of biochemical reactions. It should be noted, however, that not all enzymes are 100% selective. Proteases, for instance, can freely bind to many substrates with similar chemical structures, reducing their efficiency. Thus, it is essential to consider these potential limitations when attempting to develop biocatalytic processes. To address this issue, enzymes can be engineered to be more selective by altering the active site of the enzyme or by introducing allosteric regulation. Additionally, enzymes can be used in combination with substrate-binding proteins to increase their selectivity. Biocatalysis selectivity is enhanced by localizing the enzyme reaction to a specific compartment or environment (Zakharchenko et al. 2018 ). Gene expression regulates enzyme concentration chemically. For example, the composition and sugar content of the fruit varies according to species, stage of development, and variety. Genetic control of sugar metabolism to improve fruit quality is essential (Desnoues et al. 2016 ). Therefore, biocatalysis selectivity can be improved by regulating gene expression according to the environment, resulting in improved fruit quality.

Potential probiotics and starters

A probiotic is a live microorganism that provides health benefits to its host when administered in sufficient amounts. In order to grow and form colonies in the digestive tract, probiotics must be resistant to stomach acid and bile (Saad et al. 2013 ). It is generally understood that probiotics are derived from a heterogeneous group of LAB (Lactobacillus, Enterococcus) and Bifidobacterium genera, such as lactic acid bacteria and those commercially available for human consumption. Although yeasts play a major role in food and are widely distributed, they have not yet been well investigated as potential probiotic candidates. As probiotics, yeasts and other microbes are also being developed (Kim et al. 2019 ; Suez et al. 2019 ). Foods containing such bacteria belong to the functional foods category, which describes foods that have a health benefit. In the 1980s, Japan first used the term "functional food" to describe foods enriched with ingredients that have physiologically beneficial effects (Topolska et al. 2021 ). As well as producing proteinaceous antimicrobial agents, LABs also produce bacteriocins. Bacteriocins are peptides that exhibit antibacterial activity against food spoilage organisms and foodborne pathogens but do not affect producer organisms (Moradi et al. 2020 ). Clinical relevance of probiotics was first reported in the literature for the treatment of diarrhea, ulcerative colitis, and pouchitis. There are two critical factors when choosing a probiotic candidate regarding potential health benefits. Viability and quantity upon ingestion, survival and stability in the digestive system (Di Cagno et al. 2020 ). Vera-Pingitore et al. ( 2016 ) identified strain L. plantarum Q823 as a viable probiotic candidate for use during fermentation of quinoa-based beverages. Despite growing in quinoa-based products, this strain survives and colonizes the human GI tract.  Akkermansia muciniphila  has attracted excessive attention recently and is considered a potential probiotic because other studies demonstrated a causal relationship with obesity, inflammation, cancer, and metabolic abnormalities (Dao et al. 2016 ). As integral commercial starter cultures, LABs play an essential part in food fermentation by breaking down carbohydrates into more minor metabolites, including lactic acid, acetic acid, or carbon dioxide. Fermented food manufacturers can get starter cultures readily available in a highly concentrated form or create a custom culture. Selecting the proper factory is determined by the quantity of products that need to be produced. Factors such as the level of automation, microbiological expertise, production costs, and economic considerations all come into play.

Additionally, microbial starter cultures play a crucial role in maintaining a product's quality and functionality, including taste, texture, pH, and alcohol content (Bachmann et al. 2015 ). Industrial food fermentation uses lactic acid yeast, and ongoing research is focused on improving them (Table 2 ). A starter medium should have desirable properties such as durability in process, rapid growth, high biomass and yield, and specific organoleptic characteristics (Smid and Kleerebezem 2014 ).

Utilization of extremophiles in fermentation

The term “extremophile” describes organisms that survive under challenging environmental circumstances (temperature, pH, salinity, and pressure) and is receiving significant interest due to their capacity for catalyzing reactions and the possibility of practical utilization in extreme environments (Gupta et al. 2014 ). Among the substrates they address are acidophilic, alkaliphilic, halophilic, xerophilic, thermophilic, psychrophilic, methylotrophs, and gaseous substrates (Adebo et al. 2017 ). It is imperative that a practical approach to controlling aflatoxin B1 (AFB1) is developed, as its presence in food can be a serious health concern. Thermophiles can also contaminate food. Powdered milk products can be contaminated by Anoxybacillus flavithermus and Geobacillus spp. (Irwin 2020 ). Lactase activity is lacking in Geobacillus thermoglucosidasius and it grows slowly in fat-free milk, dependent on A. flavithermus presence to provide them with glucose and galactose for growth (Zhao et al. 2018 ). They deliver appropriate nutrients and other substances, such as beta-carotene, which can be used as a pigment or to provide vitamin A, as do Halophiles.

Furthermore, they can spoil highly acidic foods with low water activity, such as  Debaryomyces hansenii , an extremophilic yeast. As D. hansenii outcompetes unwanted microorganisms for nutrients and produces antimicrobial metabolites, both extracellularly and intracellularly, it inhibits the germination of Clostridium butyricum and C. tyrobutyricum in cheese brines. The ability of D. hansenii to multiply in cheese and its ability to consume lactate, citrate, lactose, and galactose make it an excellent starter culture for producing cheese.

Furthermore, several reports indicate that D hansenii enzymes may be active in meat fermentation, but they had minimal influence on the formation of volatile substances essential for aroma production in garlic-flavored fermented sausages and model mince (Krüger et al. 2018 ). In fermented foods, extremophilic lipases and esterases hydrolyze glycerols and fatty acids to produce polyunsaturated fatty acids. Additionally, piezophilic extremozymes are also useful for fermented food products that require high pressure (Zhang et al. 2015 ).

Fermented dairy products

Fermented foods, especially dairy, represent a rapidly expanding sector of the global food market, making it imperative to recognize and understand dairy fermented foods in the past and present (Kaur et al. 2022 ). The word “ferment” derives from Latin “fervere”, which means to boil, and is defined as “the chemical breakdown of a substance by bacteria, yeast or other microorganisms, typically by foaming and releasing heat”. Fermented foods are the products of controlled microbiological growth and enzyme transformations of food ingredients, and fermentation is a deliberate and controlled method of achieving desired qualities (Marco et al. 2021 ). Fermentation is the breakdown of organic molecules into simpler forms by microorganisms (Sharma et al. 2020 ). By introducing certain microorganisms, fermentation can produce desired flavors and aromas, as well as enhance the nutritional value and shelf-life of foods. In addition, fermentation can help preserve foods by producing antimicrobial compounds, such as lactic acid, which can prevent spoilage.

Fermented dairy products fall into two categories: traditional and non-traditional (Kroger et al. 1992 ). Conventional fermented dairy products were first produced approximately 10,000–15,000 years ago, when human lifestyle changed from gathering food to producing it (Bintsis and Papademas 2022 ). This change was due to the domestication of animals and the use of their milk as a food source. The fermentation process was used to preserve the milk and make it more palatable. This allowed for the production of a variety of dairy products such as cheese, yogurt, and kefir. Societies during the Neolithic period consciously preferred to consume different animals' milk for cultural and taste reasons and processed this milk in various ways (Charlton et al. 2019 ; Salque et al. 2013 ). Traditional fermentation has been employed for centuries in raw milk processing. The process is spontaneous, and part of the fermented product is used to inoculate the new batch (Galli et al. 2022 ). In contrast, non-traditional fermented milk products have recently been developed. These products are produced with known microbial cultures based on scientific principles, and their quality can be optimized (Galli et al. 2022 ; Kroger et al. 1992 ). Non-traditional fermented milk products are more consistent in quality as the addition of known microbial cultures creates a more controlled fermentation process. This process also ensures that the products are standardized and free of any potential health risks associated with raw milk. It has been reported that probiotic-based fermented functional foods are becoming increasingly popular since the early 2000s (Kaur et al. 2022 ). From the past to the present, fermentation practices have been influenced by various factors such as raw materials, climatic conditions, production area, social, cultural, religious, and economic aspects (Galimberti et al. 2021 ). These factors have helped to shape the diversity of fermented products, and have also helped to influence the consumption of probiotic-based fermented functional foods. The popularity of these foods has been further strengthened by the health benefits associated with them, such as improved digestion, increased nutrient absorption, and enhanced immunity. Milk and dairy products are now consumed worldwide, primarily in pasteurized and fermented forms. However, variations in consumption rates are caused by per capita income and the impact of regional preferences (Muunda et al. 2023 ). This is due to the fact that those with higher incomes can afford to purchase more nutrient-rich foods and have access to a variety of different ingredients to choose from. Additionally, regional preferences play a significant role in the demand for certain food items, as people’s taste and cultural preferences vary from one region to another.

Fermented foods with live microorganisms include yogurt, kefir, cheeses, miso, natto, tempeh, kimchi, kombucha, and some beers (Voidarou et al. 2021 ). Some foods are subjected to pasteurization, smoking, baking, or filtering after fermentation, causing live microorganisms to die or be removed. Sourdough bread (baked), shelf-stable pickles (heated), sausages (heated), soy sauce (heated), vinegar (heated), most beers, distilled spirits (filtered), coffee and chocolate beans (roasted) are fermented products (Li et al. 2022 ). Still, microorganisms have died or been eliminated from fermentation. Foods such as fresh sausages, vegetables preserved in brine or vinegar, processed soy sauce, non-fermented dried meats and fish, and acidified cottage cheese are not considered fermented, as live microorganisms are not involved in production. Fermented foods are sometimes called “probiotic foods” or “probiotics” and are used interchangeably. However, using these definitions interchangeably is incorrect (Marco et al. 2021 ). Probiotics contribute to their beneficial effects when administered in sufficient quantities. They do not have to take a specific form to have a positive effect on the host. Probiotics are live microorganisms that have a beneficial effect on the host, while fermented foods are simply foods that have gone through a process of fermentation (Dahiya and Nigam 2022 ). The probiotic benefits of fermented foods come from the live microorganisms present in the food, which are not always present in sufficient quantities to have a positive effect on the host. Molecular components of probiotic-containing foods show prophylactic or therapeutic effects against disease-causing agents. These foods are generally known as nutraceuticals, foodiceuticals, functional foods, or medifoods (Kaur et al. 2022 ). These foods interest consumers based on their nutritional and organoleptic properties and beneficial effects on human health (Luz et al. 2021 ). The effects of these foods are attributed to the presence of bioactive compounds, which can be of plant or microbial origin. These compounds, such as antioxidants, polyphenols, vitamins, and minerals, have protective effects against disease-causing agents like bacteria and viruses.

The fermentation process produces large quantities of lactic acid, alcohol, or acetic acid that inhibit other microorganisms. They also continue to reproduce unaffected by these generated substances, a process known as “amensalism” (Teng et al. 2021 ). These by-products generated by the fermentation process are toxic to other microorganisms, making them unable to reproduce. This gives the fermenting microorganisms a competitive advantage, allowing them to outcompete other microorganisms in the environment. Fermented products are usually thicker than milk because acid precipitates milk proteins. Pathogens are inhibited by high acidity and low pH (Kumar 2017 ). Fermented dairy products have a unique, desirable flavor, texture, aroma, and improved digestibility compared to the raw materials they produce (Bintsis and Papademas 2022 ). However, the wrong fermentation process poses a health hazard. Unhygienic conditions or improper food production lead to contamination and spoilage. Foodborne disorders are brought on by spontaneous fermentation by unidentified microbes, which promotes the growth of undesired and even hazardous microorganisms (Teng et al. 2021 ). This can cause food to be unsafe to eat, leading to food poisoning. Symptoms of food poisoning can range from mild to severe, and can even be life-threatening. Therefore, it is important for food producers to take proper steps to prevent contamination and spoilage.

Propionic acid bacteria (PAB) and lactic acid bacteria (LAB) are microorganisms utilized to make cheese and other fermented dairy products. LAB is used to acidify milk, and PAB is used for its aromatizing properties (Thierry et al. 2015 ). Propionic acid bacteria are microorganisms that produce propionic acid and are involved in producing fermented propionic cheeses, such as Swiss cheese, with exceptional adaptability to technological and physiological stress conditions. The propionic acid fermentation in cheese causes characteristic pores, cracks, and a slightly sweet flavor (Antone et al. 2022 ; Bücher et al. 2021 ). Propionic acid bacteria are also responsible for the formation of carbon dioxide during the fermentation process, which gives cheese its airy, spongy texture. This also contributes to the flavor of the cheese, as the carbon dioxide imparts a slightly sour taste. Propionic acid bacteria metabolism differs significantly from lactic acid microorganisms. It is characterized by the production of carbohydrates during fermentation, except for lactic acid, propionic acid, and acetic acid (Vakhrusheva et al. 2022 ). As a result of PAB's metabolic activities, the product is enriched with organic acids, vitamins (B2, B12, K, and folate), and other nutrients, increasing the stability and nutritional value of food products (Antone et al. 2022 ). Fermented dairy products provide an ideal environment for probiotic bacteria to grow in the human gut. LAB include Lactobacillus , Streptococcus , Lactococcus , Bifidobacterium , Leuconostoc , Enterococcus , and Pediococcus , which are among the most common strains of probiotic bacteria found in fermented dairy products (García-Cano et al. 2019 ; Kaur et al. 2022 ). In addition, yeasts and molds such as  Debaryomyces, Kluyveromyces, Saccharomyces ,  Geotrichum, Mucor, Penicillium , and  Rhizopus  species are employed as fermenting microorganisms (Sharma et al. 2020 ). Fermented milk products are prepared using different starter cultures, and the types of microorganisms used in production are specified in the regulations (Table 3 ). Fermentation preserves probiotic properties while maintaining microbial viability and production (García-Cano et al. 2019 ; Kaur et al. 2022 ) . This helps to ensure that the fermented milk products are safe to consume and that they have the desired probiotic properties. This is because the starter cultures help to control the growth of unwanted microorganisms while promoting the growth of beneficial ones.

Due to their resistance to low pH, adaptability to milk and other foods, and GRAS (generally recognized as safe) status, Lactobacillus species are also widely used (Galli et al. 2022 ). LAB are intentionally added to the product as starter cultures to reduce the ripening period and improve sensory characteristics such as color, flavor, aroma, and texture (García-Cano et al. 2019 ). Furthermore, food digestibility and product safety are enhanced by LAB fermentation due to the inhibition of spoilage and pathogenic bacteria. Certain LAB strains are considered probiotics because of their positive effects on the gastrointestinal system and human health and their significant roles (García-Cano et al. 2019 ). Lactic acid bacteria regulate the release of fatty acids. These properties of LAB involve metabolic processes involving enzymes such as lipases, proteases, and antibacterial proteins (Galli et al. 2022 ). Fermentation of yogurt and cheese results in a pH decrease due to the synthesis of metabolites such as organic acids, lactic acid, hydrogen peroxide, bacteriocin, diacetyl, acetaldehyde, and reuterin (Akbar et al. 2019 ).

Lactic fermentation and alcoholic fermentation are the two main types of fermentation carried out by microorganisms in fermented milk products, respectively (Galli et al. 2022 ). In lactic fermentation, lactic acid bacteria are the dominant species. Lactic fermentation products are classified according to LAB characteristics as mesophilic fermented milk, such as buttermilk, thermophilic products, such as yogurt, acidophilic milk, and probiotic products. Alcoholic fermentation occurs in products such as kefir, kumys, and Viili by yeasts and lactic acid bacteria (Galli et al. 2022 ). Microbial cultures, particularly those having proteolytic activity, are frequently employed in the dairy industry to produce cheese, yogurt, kefir, and other so-called fermented milk products. In manufacturing cheese, proteolytic enzymes are used to coagulate milk proteins and hydrolyze proteins. Proteolytic enzymes extract protein hydrolysates from milk to produce easily digestible dairy products (Kieliszek et al. 2021 ). Proteases produced by lactic acid bacteria used in lactic fermentation are capable of reducing milk protein allergens, depending on the strain and the proteolysis process. Lactic acid bacteria are a good source of hydrolyzing allergenic proteins in milk, and one isolate ( Enterococcus faecalis VB43) was reported to be an excellent potential agent for the production of hypoallergenic dairy products (Biscola et al. 2018 ). Lactic acid bacteria use β-galactosidase to hydrolyze lactose into glucose and galactose. The hydrolysis of lactose lowers the intestinal pH and promotes the production of lactic acid, which inhibits the growth of microorganisms that cause putrification (Gholamhosseinpour and Hashemi 2019 ; Sharma et al. 2020 ). Furthermore, lactic acid is essential for calcium absorption and developing organoleptic properties (Sharma et al. 2020 ). The bioavailability of minerals such as calcium, potassium, zinc, magnesium, magnesium, potassium iodide, and phosphorus is increased due to the fermentation process of lactic acid bacteria and acidity (García-Burgos et al. 2020 ).

Several studies are currently being carried out that may be useful for isolating new probiotics and developing fermented milk products with probiotic properties. Luz et al. ( 2021 ) examined seven LAB strains isolated from breast milk for their probiotic properties and used  Lactobacillus plantarum  5H1 and  Lactobacillus plantarum  5L1 strains in the production of probiotic fermented milk. LAB strains have a wide range of antimicrobial activity against pathogenic bacteria and toxicogenic fungi. During the milk fermentation process, an increase in lactic acid content, a decrease in milk pH, and an increase in total bacterial count were observed. During storage, LAB viability in fermented milk remained at 8-log 10 CFU/mL.  Lactobacillus plantarum  5H1 and  Lactobacillus plantarum  5L1 exhibited significant antimicrobial activity, sensitivity to antimicrobials, a broad spectrum of enzymatic activity, adhesion to Caco-2 cells, and reduction of  Salmonella enterica  adhesion. Furthermore, these selected strains remained viable during fermented milk storage and fermentation at 4 °C. This indicates that these strains are extremely hardy and have the potential to be used as probiotics that can survive through the fermentation and storage process.

The ability of microorganisms in fermented milk products to benefit the host is dependent on the presence of sufficient numbers of probiotic microorganisms in various products as well as the ability of adequate numbers of live microorganisms to reach the human intestine (Farahmand et al. 2021 ; Ranadheera et al. 2012 ). Thus, the legislation specifies the minimum number of live microorganisms that must be present in fermented milk products. The total number of microorganisms forming the starter culture used in products named fermented milk, yogurt, alternate culture yogurt, acidophilus milk, kefir, and kumys should be at least 107 CFU/g, the number of yeasts should be at least 104 CFU/g, and the label should be at least 106 CFU/g (Mukherjee et al. 2022 ). The number of live probiotics during the shelf life of fermented dairy products varies depending on many factors. These factors include the temperature of storage conditions, hydrogen peroxide (H 2 O 2 ) produced by other bacteria present, dissolved oxygen content due to processing conditions, pH of the end product, acidity, and strain variation. In particular, the decrease in pH during storage, the presence of dissolved oxygen, and the presence of preservatives in the final products are the major factors contributing to the loss of cell viability (Farahmand et al. 2021 ; Terpou et al. 2017 ). At the end of their shelf life, 22 of 36 commercial probiotic fermented milk products sourced from the UK and European markets (61.1%) contained more than 106 CFU/g of  Lactobacillus  strains in accordance with the minimum recommended therapeutic level for probiotics. Rep-PCR was used to differentiate the isolated strains using the GTG-5 primer, and the isolated  Lactobacillus  species were identified as  Lactobacillus acidophilus, Lactobacillus casei , and  Lactobacillus paracasei  (Farahmand et al. 2021 ). Another study found many areas for improvement in the number of cultures and accuracy of label information in commercial kefir products. More qualified controls of fermented foods are needed to demonstrate and understand their potential health benefits for humans. Consumers should demand higher levels of accuracy and quality, and regulatory bodies should conduct regular checks on these products (Metras et al. 2021 ). The antibacterial activity of LAB in fermented milk samples against  Salmonella typhimurium, Staphylococcus aureus, Escherichia coli , and  Listeria monocytogenes  was determined. L. lactis  subsp.  lactis  had a broader antimicrobial spectrum than the other isolates, and the probiotic evaluation of  L. lactis  showed that it could survive at low pH (pH 3) and 0.3–3% bile salts. It was concluded that LAB with antimicrobial activity is promising against food spoilage and pathogenic microorganisms in foods (Akbar et al. 2019 ). Hikmetoglu et al. ( 2020 ) reported that the microbial content ( Lactobacillus  spp.,  Lactococcus  spp.,  Lactobacillus   acidophilus ,  Bifidobacterium  spp., and yeasts) of traditional kefir increased during fermentation and did not change significantly during cold storage of 7 days. Lactose content decreased during fermentation, while lactic acid gradually increased and remained constant during storage. Galactooligosaccharides in kefir samples were found to be stable during storage. The major LAB species isolated and identified from traditional fermented milk in Ghana based on 16S rRNA gene sequencing were  Ent. faecium, Lb. fermentum, Lb. plantarum , and  Pd. acidilactici  (Motey et al. 2021 ).

Consumers can choose from a variety of fermented milk products. There are a few homemade products among them, but most are manufactured industrially. A variety of fermented milks and derivatives have been developed around the world, each with its own history. The type of milk used, the pre-treatment of the milk, temperature, fermentation conditions, and subsequent technological processes greatly influence their nature. The type of milk used can affect the flavor, texture, and overall characteristics of the fermented milk product. Pre-treatment of the milk can also influence the flavor, such as pasteurization or homogenization. Temperature and fermentation conditions can also have an effect, such as the length of fermentation and the type of starter culture used. Finally, the post-treatment processes, such as packaging and storage, can influence the shelf life and other characteristics of the product. Curd, yogurt, cheese, and kefir are among the most popular dairy foods (Kumar 2017 ).

Curd is a dairy product obtained by souring milk or decomposing it after adding any acidic substance. In some cases, it can also be made by mixing milk with acidic substances like lemon juice or vinegar. The liquid part is whey, and the solid part is curd. Whey contains the whey proteins of milk, while curd comprises milk proteins or casein (Kumar 2017 ). Traditionally, the curd is prepared from raw milk or boiled milk. Raw milk can undergo natural fermentation without adding any microorganisms, while boiled curd is prepared by inoculating boiled milk from the previous batch for fermentation (Joishy et al. 2019 ). It was determined that the main bacterial genera in the curd obtained from boiled milk were  Lactobacillus, Leuconostoc, Lactococcus , and  Acetobacter . In contrast, the leading bacterial genera in the curd obtained from raw milk were  Chryseobacterium, Enterococcus, Lactobacillus, Leuconostoc, Lactococcus, Streptococcus, Klebsiella, Acinetobacter, Pseudomonas,  and  Enhidrobacter.   Lactococcuslactis  subsp.  cremoris  dominated the curd obtained from both raw and boiled milk. Moreover, several metabolites such as 10-methyl dodecanoic-5-olide, ascorbic acid, and 2,2,4-trimethyl-1,3-pentanediol diisobutyrate were significantly higher in curd produced from raw milk, while dodecanoic acid and glycerol 2-acetate were substantially higher in curd produced from boiled milk.  Lactobacillus  strain and metabolites detected in curd samples were farm-specific (Joishy et al. 2019 ).

Yogurt is milk's lactic fermentation product. Lactic acid fermentation is the process by which lactic acid bacteria convert milk sugar, lactose, into lactic acid, lowering the pH. Acidification is a key mechanism responsible for coagulation during yogurt fermentation (Muncan et al. 2020 ). The casein proteins that make up the gel matrix are responsible for the thick structure of the yogurt after it has been coagulated. Casein micelles in milk exist as a colloidal calcium caseinate phosphate complex. The acidification of the milk, i.e., the lowering of the pH, leads to the dissolution of the colloidal calcium phosphate and the release of the casein content from the milk. First, at the beginning of acidification, when the pH value is reduced from 6.7 to 6, only a small amount of colloidal calcium phosphate is dissolved, so structural changes in micelles are limited. When the pH is reduced to 5, the colloidal calcium phosphate is completely dissolved, and when the pH drops to the isoelectric point of casein (pH 4.6), casein micelles aggregate and form the yogurt gel matrix (Muncan et al. 2020 ). The yogurt cultures  Lactobacillus delbrueckii  subsp.  bulgaricus  and  S. thermophilus  have a symbiotic relationship and produce yogurt with an excellent taste, acidity, and viscosity.  L. delbrueckii  subsp. bulgaricus can readily utilize pyruvic acid, formic acid, folic acid, and long-chain fatty acids produced by  S. thermophilus , while  L. delbrueckii  subsp. bulgaricus contributes to S. thermophilus growth (Dan et al. 2017 ). Furthermore, the volatile compounds produced by lactic acid bacteria significantly influence the flavor of the products. The flavor comprises a variety of volatile compounds, including acids, aldehydes, alcohols, ketones, esters, and aromatic hydrocarbons, and each class has its organoleptic properties (Dan et al. 2017 ; Farag et al. 2022 ). Yogurt is not a probiotic food, but it contains non-probiotic bacteria from milk fermentation. However, probiotic yogurt can be obtained by adding probiotic bacteria. Also, yogurt products obtained from a mixture of probiotics ( L. rhamnosus  GG) and prebiotics (dietary fiber) can be received (Kaur et al. 2022 ). The probiotic bacteria in yogurt contain beneficial bacteria that can help to support the good bacteria already present in the body. They can help to restore the balance of bacteria in the gut, which can help improve digestion and overall health. Prebiotics, on the other hand, are dietary fibers that act as food for the beneficial bacteria, helping them to thrive and grow in the gut. Therefore, combining probiotic bacteria with prebiotics can help to create a more beneficial environment in the gut.

Kefir is acidic-alcoholic fermented milk formed by the fermentation of milk by cauliflower-like kefir grains or starter microorganisms containing lactic acid bacteria, acetic acid bacteria, and yeasts, and is different from other fermented products due to the specificity of starter microorganisms (Al-Mohammadi et al. 2021 ; Bengoa et al. 2019 ; Fatahi et al. 2021 ). Kefir grains are white or light yellow in color, elastic in consistency, 0.3 to 3.5 cm in diameter, and composed of protein and polysaccharides (Al-Mohammadi et al. 2021 ; Bengoa et al. 2019 ). Kefir grains comprise approximately 83% water, 4 ± 5% protein, and 9 ± 10% a polysaccharide called kefiran (Bengoa et al. 2019 ). During fermentation, lactic acid, acetic acid, ethanol, carbon dioxide, organic acids, amino acids, vitamins (E, B3, B6, and B12), minerals (Se, Fe, Zu, and Mn), and enzymes (glutathione peroxidase, catalase, and superoxide dismutase) are formed (Fatahi et al. 2021 ). The pH of kefir ranges between 4.2 and 4.6, the ratio of ethanol between 0.5 and 2.0%, the ratio of lactic acid between 0.8 and 1%, and the ratio of CO 2 between 0.02 and 0.2% (Rosa et al. 2017 ). Kefir inhibits pathogenic bacteria and fungi, and the inhibitory activity is more robust against bacteria (Al-Mohammadi et al. 2021 ). The antimicrobial activity of kefir and probiotic yogurt samples produced from cow, camel, sheep, and goat milk was investigated. It was determined that kefir samples had more substantial antifungal and antibacterial effects than probiotic yogurt samples, and kefir and yogurt samples produced from sheep and cow milk showed the highest and lowest antimicrobial activity against  S. aureus, E. coli, S. enterica,  and  L. monocytogenes , respectively.  A. niger, S. aureus,  and  L. monocytogenes  were the most susceptible microorganisms, while  Penicillium spp .  and  E. coli  were the most resistant. Bioactive substances, organic acids, ethyl alcohol, hydrogen peroxide, diacetyl, peptides, possibly bacteriocins, and other inhibitory compounds have been suggested to be responsible for inhibiting the growth of pathogenic bacteria (Azizkhani et al. 2021 ).

Kumys is a fermented milk product made by fermenting mare's milk in two stages with bacteria and yeasts: lactic fermentation and alcoholic fermentation. The mare’s milk to be used in kumys production should have an acidity of ≤ 0.06% lactic acid, a density of 1029–1033 g/mL, and a fat content of at least 1% (Kondybayev et al. 2021 ). Fermentation is 1–3 days at about 20 °C (Liu et al. 2019 ). The consistency of kumys is a liquid, homogeneous, carbonated, slightly foaming drink without any fat particles (Kondybayev et al. 2021 ). The products of kumys fermentation are lactic acid, ethyl alcohol (0.6–3%), carbon dioxide, and other by-products such as volatile acids, alcohols, and other compounds with strong and distinctive aroma and taste (Afzaal et al. 2021 ; Kondybayev et al. 2021 ). According to the lactic acid content, three types of kumys are defined: strong, medium, and light (Afzaal et al. 2021 ). The fermentation time of kumys does not affect its quality. Milk from fresh mares and mature kumys had the highest chemical and nutritional content, while immature kumys (fermentation time less than 9 h) was not good quality (Liu et al. 2019 ). The microbiota of raw mare’s milk has a higher microbial diversity than that of kumys. Raw mare's milk is rich in LAB, such as  Lactobacillus helveticus, Lactobacillus plantarum, Lactococcus lactis,  and  Lactococcus kefiranofaciens . In contrast, raw mare's milk contains pathogenic bacteria such as  Staphylococcus succinus, Acinetobacter lwoffii, Klebsiella oxytoca,  and  Klebsiella pneumoniae.  The change in microbiota composition and structure could be attributed to the transition from a slightly alkaline environment in raw mare's milk to a highly acidic kumys environment. The acidic environment in kumys inhibited the growth of most environmental pathogens, increased food hygiene, and minimized the risk of infection by endogenous pathogens found in raw mare’s milk (Zhang et al. 2020b ).

Fermented foods are also valued for their improved shelf life, safety, nutritional value, and other properties, and are the most widely consumed by humans (Walhe et al. 2021 ). Fermented dairy products have several health benefits when consumed regularly and in a balanced and appropriate proportion (Kaur et al. 2022 ). The various health benefits of yogurt, cheese, kefir, and other traditional fermented milk products have been extensively researched. Probiotic strains of bacteria present in fermented dairy products are beneficial for gut health and can reduce the risk of certain diseases (Okoniewski et al. 2023 ). Additionally, fermented dairy products are a rich source of vitamins and minerals, including calcium, potassium, phosphorus, and B vitamins. Fermented dairy products are an effective treatment method that contains natural ingredients with high nutritional and digestibility, anti-hypertensive, hypo-cholesterolemic, antioxidant, immunomodulatory, and anti-inflammatory properties and fewer adverse side effects (García-Burgos et al. 2020 ). Probiotic consumption has been shown to positively affect the reduction of ailments from diarrhea to cancer (Akbar et al. 2019 ). Regular kefir consumption has been linked to benefits for lactose intolerance and the digestive system, as well as antibacterial, antihypertensive, anti-inflammatory, hypo-cholesterolemic effects, plasma glucose control, antioxidant, anticarcinogenic, antiallergenic activity, and wound healing (Rosa et al. 2017 ). Koskinen et al. ( 2018 ) found that low-fat fermented dairy consumption was inversely correlated with cardiovascular disease risk. However, cardiovascular disease risk has been reported with very high consumption of unfermented dairy products and milk. Zhang et al. ( 2020a ) stated that fermented dairy products reduce cardiovascular disease risk. (Lee et al. 2020 ) reported that  Lactobacillus plantarum  B719 can be used as an alternative in treating primary postmenopausal osteoporosis. (Fatahi et al. 2021 ) At 24 and 48 h, the interactions between different concentrations of kefir drink and U87 cancer cells (glioblastoma), the most severe form of brain tumor, were evaluated. As a result, it was discovered that kefir significantly reduced the growth rate of U87 cells at increasing concentrations and had a killing effect. It could be used as a complementary treatment.

Companys et al. ( 2021 ) reported that consuming fermented dairy products reduces the risk of stroke and cardiovascular diseases, and consuming yogurt reduces the risk of developing type 2 diabetes mellitus. However, there is insufficient evidence that fermented milk or cheese consumption protects against metabolic syndrome. It is stated that the available evidence on the effect of dietary cheese and yogurt on hypertension is limited and that consumption of smoked cheeses should be limited in hypertensive patients due to their high sodium content. Walhe et al. ( 2021 ) isolated three isolates with probiotic potential ( Enterococcus faecium (EF), Enterococcus faecium (Chole1), and  Lactobacillus pentosus  (7MP) from yogurt and determined that among these three isolates,  Enterococcus faecium  (EF) and  Enterococcus faecium  (Chole1) produced vitamin B12 in a fair amount (1 ng/mL); whereas,  Lactobacillus pentosus  (7MP) had the highest cholesterol reduction potential (48%) compared to the others.

Fermented meat products

Meat fermentation is an ancient preservation method widely used to increase meat products’ taste, aroma, palatability, color, tenderness, and shelf life. Meat is exposed to microorganisms or enzyme activities during fermentation, so desirable changes occur in meat biochemistry. The process of fermentation causes proteins and fats to break down, resulting in a more tender meat product and a more intense flavor (Wang et al. 2022 ). The breakdown of proteins and fats also helps to protect the meat from spoilage, thus increasing its shelf life. Meat physicochemical, biochemical, and microbiological changes run the fermentation process and support the formation of desirable meat products (Kumar et al. 2017 ). The fermentation process is an essential metabolic process converting carbohydrates into acids, gases, and alcohol, resulting in the conversion of raw meat to fermented meat products through the activities of “cultured” or “native” microorganisms (Kumar et al. 2017 ). This is because the anaerobic environment formed during the fermentation procedure encourages the growth of some lactic acid bacteria strains (Ravyts et al. 2012 ). These bacteria strains produce lactic acid that gives fermentation products their distinctive flavor and texture. Lactic acid also acts as a natural preservative, extending the product's shelf life. Fermentation of meat products is performed by lactic acid bacteria on a “native culture” or “starter culture”. Using native flora for meat fermentation may cause many problems, including inconsistent quality. This problem was solved by cultivating a commercial starter culture in a controlled environment to maintain the same quality (Kumar et al. 2017 ). Pediococcus cerevisiae  was the first starter culture for meat fermentation (Deibel et al. 1961 ). Then, the other species are  Lactobacillus sakei  and  Lactobacillus curvatus  among the LAB,  Staphylococcus xylosus , and  S. carnosus  among the coagulase-negative staphylococci and  Debaryomyces hansenii  among yeasts were also used for meat product fermentation (Alessandria et al. 2014 ). LABs produce bacteriocins that improve meat quality and stability during fermentation. Bacteriocins are proteinaceous compounds that exhibit antibacterial activity against pathogens. Bacteriocins show bactericidal effects except for eukaryotic cells and are also tolerant of heat and salt (De Vuyst and Leroy 2007 ). This means that when these compounds are added to the fermentation process, they can help to inhibit the growth of harmful bacteria while also preserving the flavor of the meat. Furthermore, the heat and salt tolerance of bacteriocins ensures that the meat will remain safe for consumption for a longer period of time.

Sausages, dating back to 1500 BC, are the most popular and oldest meat products consumed globally because of their flavor and nutritional function. Generally, sausages are produced from salted minced or chopped meat. They are formed by filling seasoned raw meat with starter cultures into natural or artificial casings, then hanging them to ferment and ripen (Kumar et al. 2017 ). The starter culture is typically a single LAB species or a LAB mixed with other bacteria ( Staphylococcus xylosus  or  S. carnosus ) (Holck et al. 2017 ).

Microbial spoilage in fermented meats

Microorganisms found in the meat microbiota interact with each other and meat substrate during processing and storage. A small percentage of these microorganisms growing on meat can deteriorate foods through their metabolic activities. For instance, lactic acid bacteria (LAB) produce lactic acid from meat carbon sources. Lactic acid produced by LAB has various positive and negative effects based on the kind of meat product (Lahiri et al. 2022 ). It also helps to form desirable changes in fermented meats, such as an acidic taste and decreased pH. However, it may cause undesirable changes in other products. Thus, microbial spoilage is a highly complex structure with varying properties depending on the microorganism, substrate, and the nature of the fermented product. Although several microbial metabolic pathways are known that lead to changes in the taste, color, odor, or texture of meat products and stimulate the generation of defined spoilage compounds, the primary mechanism that leads to spoilage still needs to be fully resolved. Therefore, to understand this mechanism that leads to meat spoilage, it is essential to initially comprehend the microbial factors of meat, their interactions, and metabolic activities (Zagorec and Champomier-Vergès 2023 ). To understand the primary mechanism that leads to meat spoilage, it is important to analyze the microbial components of meat, their interactions, and their metabolic activities. This will help to identify the pathways and mechanisms that lead to spoilage and can help improve food safety and quality.

Mycotoxins in fermented meat

Meat and meat products can be contaminated with toxic compounds, such as mycotoxins, during production, storage, and distribution (Pleadin et al. 2021 ). Mycotoxins contamination in the final product can be related to raw materials, spices, additives used in production, or hazardous environmental components. Therefore, these toxic components that cause contamination can adversely affect human health (Pleadin et al. 2016 ). Mycotoxins are produced by certain types of fungi and can be found in crops, grains, and even in animal feed. When these contaminated raw materials are used in the production of meat and meat products, mycotoxins can be passed on to the final product.

Mycotoxins are secondary metabolites produced by molds, responsible for acute and chronic toxicity of humans and animals. Mycotoxin contamination can occur in meat products in these ways; due to meats supplied from animals fed with contaminated feed, the components such as contaminated spices added to the meat products, and can arise as a consequence of the activity of molds growing on the surface of fermented meat (Alapont et al. 2014 ; Bertuzzi et al. 2013 ). Ochratoxin A (OTA) and aflatoxin B1 (AFB1) are the most common mycotoxins contaminating fermented meat products. AFB1 is the most common liver carcinogen categorized in group 1 by the International Agency for Research of Cancer (IARC).  Aspergillus flavus  and  Aspergillus parasiticus  are known as responsible species for the production of AFB1. OTA is a group 2B carcinogen, and the genus of  Aspergillus  and  Penicillium  are responsible for its production (Pleadin et al. 2021 ). Mycotoxigenic molds isolated from fermented meat products can produce mycotoxins under various conditions, such as environmental temperature, humidity, and water activity during the ripening period of meat products (Pleadin et al. 2015 ). Several studies have pointed out the possibility of the presence of mycotoxin contamination in fermented meat products as a result of inadequate control of production and storage conditions, indicating the necessity of prevention of contamination that can adversely affect human health (Alapont et al. 2014 ; Pleadin et al. 2016 ). Pleadin et al. ( 2016 ) observed significant AFB1 and OTA levels in “Slavonski Kulen” fermented sausages as 11.79 ± 2.34 µg kg –1 , 16.13 ± 3.32 µg kg –1 , respectively. OTA levels in Istrian, Slavonian, and Kulenova Seka fermented sausages were determined as 0.25 ± 0.01 µg kg –1 , 0.27 µg kg –1 and 0.26 ± 0.14 µg kg –1 , respectively (Kudumija et al. 2020 ). In another study, OTA levels in İberian ham were noticed as 3.20 µg kg –1 (Rodríguez et al. 2015 ).

Biogenic amines in fermented meat

Biogenic amines are organic compounds found naturally in many foodstuffs with an aliphatic, aromatic, or heterocyclic structure formed due to microbial decarboxylation of amino acids or the amination of aldehydes and ketones (Santos 1996 ). These compounds are formed by the action of microbial enzymes on amino acids, and they can contribute to the flavor, aroma, and texture of foods. They are also important as they can act as toxins, leading to food spoilage and safety issues.

It has been known that high-concentration exposure to biogenic amines can lead to toxic effects on respiratory and cardiovascular systems (Tsafack and Tsopmo 2022 ). Biogenic amines are more frequently found in fermented meat and meat products because of their predisposition to amine decarboxylation by the natural microbial flora. They may be produced during the fermentation stage by the activity of microorganisms while the meat proteolysis. Insufficient hygienic quality of raw material, re-contamination, and deficiencies in production and storage steps significantly impact the formation of biogenic amines (Gernah et al. 2011 ). In such circumstances, they are also used as a spoilage indicator and poor hygiene conditions for meat products. Lactic acid bacteria that have grown and displayed their metabolic activity on these fermented meat products have a crucial function in forming biogenic amines such as putrescine, cadaverine, histamine, and tyramine (EFSA 2011 ).

Biogenic amines have been reported numerous times in fermented meat products (Alves et al. 2017 ; Rabie et al. 2014 ; Sun et al. 2016 ). Alves et al. ( 2017 ) evaluated the biogenic amine levels of Portuguese and Serbian fermented dry sausages. While histamine was not detected in both sausages, cadaverine, putrescin, and tyramine were found significantly in these samples. Another study assessed biogenic amines in dry-ripened sausages made from different meats (horse, beef, and turkey). The study concluded that the total biogenic amine contents, from highest to lowest, were ranked for turkey, beef, and horse sausages, respectively. The high levels of total biogenic amines originated from the elevated histamine, putrescine, and tyramine content in turkey sausages (Rabie et al. 2014 ). Sun et al. ( 2016 ) observed the high histamine, tyramine, and cadaverine levels in traditional Chinese Sichuan-Style sausages (mean value of 196 mg/kg, 164.6 mg/kg, 141.6 mg/kg, respectively). Researchers indicated that these results were linked to poor hygiene of raw materials and insufficient hygiene conditions during processing steps. Due to the activity of microorganisms, fermented meat products contain higher levels of biogenic amines. Insufficient hygienic conditions were found to increase the amount of free amino acids present in the raw materials. These free amino acids are then available to be used by microorganisms during the fermentation process, leading to the increased biogenic amine contents of the final product.

Fermented meat products worldwide

Raw meat is a highly perishable food, and preservation of meat is a significant problem. In early civilizations, preservation techniques such as salting and drying under the sun were used for long-term meat preservation. These preservation strategies resulted in lower water activity levels, which protected the meat from spoilage and pathogenic microorganisms (Zeuthen 2007 ). Many traditional fermented meat products are consumed by different cultures worldwide because of differences in raw materials, formulations, or manufacturing processes. The low water activity levels of the salted and dried meat provided a hostile environment for microorganisms, thereby preventing the growth of spoilage and pathogenic microorganisms. This allowed the meat to be stored for a longer period of time without it spoiling. Additionally, traditional fermented meats are processed differently in various cultures, resulting in different flavors, textures, and shelf lives. These products are an essential source of information about society's consumption habits. The quality and quantity of fermented meat products produced vary by country (Kumar et al. 2017 ). Table 4 lists some common fermented meat products.

Fermentation role in alternative proteins

Fermentation of plant-based products.

Fermentation of plant-derived products was used for many decades. From a historical perspective, during the Neolithic period in 8500–400 BC, fermentation accidentally started with plant-derived products, such as grain, to produce wine-like beverages, which can preserve plant-based products longer (Lavefve et al. 2019 ). Two thousand five hundred years ago, fermented beans were discovered to produce soy sauce Asian. The list of fermented plant-based products is found in multiple countries, as shown in Table 5 . Last few decades, fermented plant-related food has become a novel food trend, although its popularity has decreased due to food industrialization, especially in European countries (Giacalone et al. 2022 ; Michel et al. 2021 ; Profeta et al. 2021 ). The interest in the last decades is due to the demand for healthy food products with healthy properties found in plant-based products (Anusha Siddiqui et al. 2022 ; Bryant and Sanctorum 2021 ; Schiano et al. 2020 ). For example, kombucha is produced from lactic acid bacteria, and acetic acid bacteria generate the product without alcohol, which is more acceptable for consumers in European countries.

Many fermented foods, as shown in Table 5 ,  are a type of traditional foods which can raise the popularity of traditional food exposure to global consumers (Anusha Siddiqui et al. 2022 ). For example, pickling is fermented by immersing vegetables in vinegar into various foods to prolong their shelf life. The pickling system process looks like the fermentation of sauerkraut using lactic acid bacteria and salted brin performed at acidic fermentation (Di Cagno et al. 2013 ; Vitali et al. 2012 ). The world's most popular pickling is the small cucumber pickled vegetable, made with lactic acid bacteria, such as  lactobacillus spp, Weissella spp , Pediococcus spp , Pediococcus sp , Leuconostoc spp , and Lactococcus spp .  The fermentation in pickling can improve the taste of the pickling products. The pickling can be produced from other plant-based products, like olives (Hamid Abadi Sherahi et al. 2018 ) and carrots (Di Cagno et al. 2013 ). Other fermented plant-based products, such as fermented peppers and soybeans, have been reported. Peppers can be fermented with high levels of acetic acid, while soybean is fermented to produce various products, including soy sauce, tofu, and tempeh. Those fermented plant-based products involve different types of microorganisms.

Lactic acid bacteria, such as  lactobacillus spp .  play an essential role in the fermentation of food products (Di Cagno et al. 2013 ; Marco et al. 2017 ). Fermentation of vegetables typically happens accidentally, called spontaneous fermentation, where fermentation occurs due to lactic acid bacteria in the cabbage. Lactic acid bacteria initiated fermentation. Other species responsible for vegetable fermentation are  lactobacillus brevis, Leuconostoc mesenteroides, pediococcus,  etc. (Di Cagno et al. 2013 ; Xiong et al. 2012 ). For this species, culture-based methods are applied to initiate fermentation. The microorganisms involved during product fermentation determine the types of products. As an example, soibum and soidon are fermented products made from bamboo shoots in Manipur, India. Soibum involves the  P. pentosaceous  and  L. plantarum , which are not used for fermenting Soidon products (Jeyaram et al. 2010 ; Yan et al. 2008 ). This also affects consumers' use of products. Soibum is typically served as a side dish, while Soidon is used as a curry mixed with potato and green chilies (Jeyaram et al. 2010 ; Mir et al. 2018 ). This difference in fermentation process and use of different ingredients results in a distinct flavor, texture, and aroma of Soibum and Soidon. As a result, consumers have different preferences for these two products, and they use them for different cooking preparations.

Fermentation of fruits

Compared to plant-based food products, fermentation fruits are generally used as a beverage. Table 6 shows a list of fermented fruits with responsible bacteria. Fermented fruit products relate to a valuable and large beneficial microorganism. The majority of the time, different native microorganisms present in the raw components spontaneously ferment diverse plant-based substances to produce fermented products. The fermentation of fruits involves lactic acid bacteria, a small part of the microbiota of raw fruits (Di Cagno et al. 2013 ). Depending on the kind of vegetable, hetero- and homo-fermentative organisms from the genera  Pediococcus, Enterococcus, Weissella, Lactobacillus,  and  Leuconostoc,  were variably detected. The most prevalent species were  Weissella cibaria/Weissella confusa  and  Lactobacillus plantarum . Fermented sweet cherries, for example, represent the alternative source of indigenous microorganisms (Di Cagno et al. 2011 ). The microbiota from the fruits is adapted to the fermented brine solution making the microorganisms isolated from an ecosystem typically having technological properties, such as resistance to salt, high acidification rates, pH, temperature, and phenolics (Di Cagno et al. 2013 ; Marco et al. 2017 ).

Other fermented fruits in Table 6  are also found in other countries with different fruit sources. Fermented cashew apples contain oligosaccharides, which can be evaluated with  Lactobacillus johnsonii  to determine the degree of polymerization. However, the fermented cashew apple is still considered to have an unpleasant taste to be consumed by humans (Vergara et al. 2010 ). The fermentation of fruit with L. johnsonii happens due to the focus on enzymatic synthesis, where glucose and fructose are used as enzyme acceptors. UK consumers drink cider, another beverage product from apples. This beverage is fermented by  L. brevis, L. paracollinoides, L. casei, L .  diolivorans . It is also under the same conditions as wine from grapes (Di Cagno et al. 2013 ). In general, fruit fermentation research is limited, whereas the fruits contain beneficial microorganisms to explore deeply to understand the importance of microorganisms isolated for the generated food products. Cider is produced by fermenting apples with certain species of lactic acid bacteria, which help to break down the fructose and glucose in the apples into ethanol. This fermentation process is similar to the process used to produce wine from grapes, although the microorganisms used are slightly different. As a result, more research is needed to better understand the role of microorganisms in fruit fermentation and their potential to generate beneficial food products.

Fermentation of cereals

The majority of fermented foods manufactured from grains are found in Africa. The natural microbiota is employed to ferment grains like maize, millet, rice, or sorghum. The grains are frequently cooked, crushed, malted, and occasionally filtered. Many well-known cereal-based products have distinctive regional variations in content and preparation (Achi and Asamudo 2019 ; Tsafrakidou et al. 2020 ). African cereal products may be divided into a few main types; liquids, porridges, (semi)solid prepared doughs, and liquid drinks, such as nonalcoholic gruels (Achi and Asamudo 2019 ).

Table 7 lists fermented cereals and microorganisms responsible for fermentation. The Burkinabe dish of ben-saalga, a thin porridge made from fermented pearl millet (Pennisetum glaucum) sediment cooked in water, is well-known in Ghana (Achi and Asamudo 2019 ; Nout et al. 1995 ). Natural fermentation is often dominated by  L. fermentum, L. plantarum,  and  P. pentosaceus,  requiring the energy density of fermented gruels derived from cereal; some  L. plantarum  strains can hydrolyze starch, which can be advantageous. Another product is Ogi, a well-known morning gruel traditionally made by naturally fermented maize grains to create a supplementary diet for kids (Achi and Asamudo 2019 ; Gupta and Abu-Ghannam 2011 ; Nout et al. 1995 ). The precise composition will impact the end product's viscosity, fermentability, and content. It can also be prepared from sorghum or millet grains. Ogi is often ingested following heat treatment, eliminating the probiotic properties of lactic acid bacteria (Gupta and Abu-Ghannam 2011 ). It must be noted that these foods’ functional properties are connected not only to how bioactive live cells interact with the host but also indirectly by ingesting bioactive chemicals generated during fermentation. Thus, natural fermentation is a viable way to promote a healthy lifestyle through the consumption of plant-based foods with antimicrobial properties.

In several African nations, alcoholic and non-alcoholic beverages are made from fermented sorghum and millet (Achi and Asamudo 2019 ). They serve as the base grains for the non-alcoholic beverage bushera and the traditional alcoholic beverage muramba.  Lactococcus, Leuconostoc, Lactobacillus, Weissella,  and  Enterococcus  are responsible for bushera production (Muyanja et al. 2003 ). While Ethiopian customers are well-versed with barley meals and beverages, including Kunun-zaki, shorba, kinche, tihlo, shamet, chuko, beso, etc., is another millet-fermented beverage that is frequently enjoyed in Northern Nigeria. Lactic acid fermentation is a typical, simple, and affordable method for processing foods, including starch, to ferment cereal products. Cereal food products’ nutritional and organoleptic value is improved through lactic acid bacteria fermentation. The sensory qualities represent the first significant advancement. Bread, loaves, confectionary, pastes, noodles, gruels, semi-digested drinks, and supplemental meals for infants and children are produced by lactic acid fermentation of cereal substrate (Tsafrakidou et al. 2020 ).

Fermentation of insects

In many civilizations worldwide, eating insects has long been a widespread practice (Anusha Siddiqui et al. 2022 ; Caparros Megido et al. 2016 ). Because of their better feed-conversion efficiency, reproductive potential, and environmental sustainability, insect-based products have gained favor as trendy new food items in addition to their excellent nutritional value (Niva and Vainio 2021 ). To enhance the sensory, nutritious, and shelf-life properties of new components and products and their availability and customer acceptance/receptivity, scientists and technologists have adopted both conventional and cutting-edge processing techniques (Caparros Megido et al. 2014 ; Mancini et al. 2019 ). With its ability to enhance fermented meals’ flavor, rheology, and texture and alter people’s perceptions of processed insect products, fermentation has attracted considerable study. Fermented sauces created with wax moth grasshoppers ( Locusta migratoria ) and larvae ( Galleria mellonella ) exhibited substantial acceptance for several sensory descriptors such as “sour”, “bitter”, “sweet”, and “umami”, when compared to a commercial fish sauce (Mouritsen et al. 2017 ). This behavior was due to increased fermentation-derived substances such as lactic acid, free amino acids, and fatty acids. There is much work to be done in order to harness the benefits of fermentation in order to enhance the sensory quality of insect-based food products and improve their availability in the marketplace. Moreover, this process may transform raw materials into biomass, fuels, and chemicals, all with a wide range of commercial uses. To treat edible insects, fermentation technology can potentially increase insect components' functioning and their use. The fermentation products of insects and bacteria are listed in Table 8 .

Compared to the fermentation of the previously mentioned items, the fermentation of insect feeds is relatively new. Cho et al. ( 2019 ) used an  Aspergillus kawachii  solid-state fermentation to treat the flour made by mulberry silkworm larvae ( Bombyx mori ). The scientists examined how fermented silkworms produced free amino acids, fatty acids, minerals, and alcoholic chemicals. In a study by Jang et al. ( 2018 ), several microorganisms were used to ferment yellow mealworm larvae ( Tenebrio molitor ,  Lactobacillus plantarum, Lactobacillus gasseri, Aspergillus kawachii, Saccharomyces cerevisiae,  and  Bacillus subtilis ). Following fermentation with each strain separately, extracts of water, ethanol, and methanol were made and used to evaluate the biological characteristics of the products.

According to the facts above, fermentation is a workable alternative to other methods of preparing active insect metabolites. These naturally occurring substances, produced by fermentation, might be utilized as components in functional foods and nutraceuticals. Due to the bioactive substances insects have produced through fermentation, they will one day provide consumers with health benefits. However, further study is needed to benefit from their future uses and numerous health benefits in the future. Indeed, fermentation offers a unique method of obtaining active compounds from insects that may be used in a variety of applications. These compounds can be used to produce medicines, vitamins, and cosmetics, among other things. They can also be used to create sustainable food products, such as protein bars, that can provide essential nutrients to those with limited access to a balanced diet.

Fermentation of seaweed

Seaweed fermentation has been previously observed in food or medicine (Gullón et al. 2020 , 2021 ; Wendin and Undeland 2020 ). The demand for seaweed in the Asian market, which has resulted in sharp increases in aquaculture yields, has been a significant factor in the continuous rise in seaweed consumption over the past few decades. Global seaweed harvesting was 29 million tonnes in 2016. Their primary uses were synthesizing hydrocolloids for food and pharmaceuticals, animal feed, and human consumption (Zhang et al. 2022 ). While early investigations indicated excellent yields, seaweeds are particularly ideal for this purpose because their development systems do not compete with crops and do not require fresh water.

Seaweed fermentation products are most pertinent because the primary structural polysaccharides undergo hydrolysis, producing a high quantity of glucose (Monteiro et al. 2021 ). Laminarin, alginate, and fucoidan are found in brown seaweeds, agar and carrageenans in red seaweeds, starch and ulvan in green seaweeds, and laminarin, alginate, and fucoidan are found in brown seaweeds (Milinovic et al. 2021 ; Pérez-Alva et al. 2022 ). Brown seaweeds provide extra fermentable sugars in the form of mannitol and glucuronic acid that, provided mannitol-fermented cultures have been used, can further enrich the fermentable mash. These sugars and the hydrolyzed polysaccharides undergo glycolysis to produce pyruvate, which is subsequently fermented to produce either lactic acid or ethanol and CO 2 , as shown in Fig.  2 . Most microbial cultures cannot use several seaweed sugars, including mannuronic and uronic acids, fucose, rhamnose, and xylose, making ethanol fermentation of seaweed difficult, so genetically modified cultures have been created to convert seaweed sugars well (Monteiro et al. 2021 ). Seaweed has an intact protein complex, hydrolyzed after fermentation. The fermentation also physically disrupts seaweed cells and consequently breakdown the protein–phenolic blends to release the Fermentation of various seaweeds depending on the sugar content in seaweeds to select the bacteria involved in the fermentation process, shown in Table 9 . Seaweed  Gracilaria verrucosa  can be fermented with  Hortaea werneckii, Lactobacillus spp .,  and S taphylococcus . The fermentation of seaweeds increased antioxidant and antimicrobial activity (Fatmawati et al. 2022 ). The increase in antimicrobial activity implicated the protection of seaweeds from pathogenic and spoilage bacteria and improved the seaweeds' nutritional value by reducing the insoluble and indigestible fractions (Maiorano et al. 2022 ). Figure  2 shows the fermentation process. The fermentation process activates the seaweeds' antimicrobial activity which helps to protect them from bacteria and other contaminants. This process also aids in the breakdown of indigestible components, making the seaweeds more bioavailable and easier to digest. This makes them ideal for use in a variety of applications, such as biofuels, nutritional supplements, and pharmaceuticals.

a Chemical fermentation path of the seaweeds, and b physical appearance of the fermentation of process in seaweeds. “Created with BioRender.com”

Furthermore, bacteria involving the fermentation process can also utilize fungi found in the marine area. Landeta-Salgado et al. ( 2021 ) reported the fermentation of green seaweeds  Ulva spp .  hydrolyzed by the marine fungi  Paradendryphiella salina . The results showed an increase in yield, protein, and amino acids. However, the research on the fermentation of seaweeds for functional foods still needs to be completed. Further analysis of fermented seaweeds’ effects on food processing is essential.

Coffee fermentation

Coffee is a widely consumed beverage prepared from coffee beans. Despite fermentation being necessary to remove the mucilage layer, subsequent heat-intensive processes (roasting and brewing) produce a drink that is close, as shown in Fig.  3 . During coffee fermentation, parchment coffee's mucilage must be removed. Coffee mucilage contains starch, cellulose, and pectin. The mucilage may make it difficult to dry coffee beans and, in rare cases, may also promote mold growth, lowering the final coffee quality (Haile and Kang 2019a ). Spontaneous fermentation is often employed since it is explicitly done to remove mucilage (Haile and Kang 2019b ).

Coffee fermentation from wet processing. Created with BioRender.com

Furthermore, coffee beans already contain all the ingredients needed to produce coffee flavor and fragrance during roasting (Joët et al. 2010 ). Yet, fermentation can broaden the variety of chemicals that give coffee flavor and fragrance, including more than 700 volatile and nonvolatile chemicals. According to reports, yeast, LAB, and Enterobacteriaceae are predominantly responsible for wet fermentation, whereas acetic acid bacteria and Pichia yeasts are responsible for dry fermentation (Lavefve et al. 2019 ), as shown in Table 6 . Since the mid-1900s, numerous microorganisms have been isolated from wet processing fermentation. Since aromatic chemicals are created when the mucilage layer in wet processing is removed, wet-processed coffee has better scent attributes than dry-processed coffee (Haile and Kang 2019a ). Current research on coffee fermentation during dry, semi-dry, and wet processing focuses on using aromatic yeasts to create flavor (De Melo Pereira et al. 2015 ; Evangelista et al. 2014 ). A wide range of microbial species (Table 10 ) are present during coffee fermentation; however, only a small number of these native microorganisms were chosen because of their potential effects on the coffee’s flavor and fragrance. Fermentation should be regulated to achieve this favorable outcome. The choice of suitable microorganisms that positively impact coffee flavor and fragrance during fermentation is crucial. Thus, it is important to properly regulate fermentation in order to achieve desired flavor and aroma in coffee. The choice of the right microorganisms is important because it is these microorganisms that produce the compounds responsible for the flavor and aroma of coffee. Therefore, by regulating the fermentation process, the desired flavor and aroma can be achieved.

Precision fermentation

Producing edible microbes has the potential to bypass many of the environmental constraints of food production and reduce its environmental footprint at a time when climate change threatens the global food production system (Linder 2019 ). The use of fermentation has been a useful method of food preservation in the past. The microbial populations involved made the resulting products typical concerning where processing occurred (Campbell-Platt 1994 ). Precision fermentation uses synthetic biology, especially genetic engineering, to insert specific genes into the DNA backbone of single-celled organisms and microorganisms to produce desired fermentation properties and products (Augustin et al. 2023 ). One way to reduce by-product formation is to create synthetic cellular factories in which all available resources are diverted to produce the compounds needed and nothing more. Known as precision fermentation or synthetic biology, the technique is now being touted as a potential alternative to traditional fermentation (Fig.  4 ). The focus is designing optimized metabolic pathways and assembling the genes involved in the microbial chassis. In order to analyze and characterize microbial genomes and metabolic functions, this technology relies heavily on artificial intelligence, bioinformatics, systems biology, and computational biology (Teng et al. 2021 ).

Precision fermentation. “Created with BioRender.com”

Recent advances based on genomics and synthetic biology include precision fermentation and biomass fermentation to produce specific compounds for food and chemical industrial or pharmaceutical purposes (Teng et al. 2021 ). A variety of vitamins are found in microbial biomass, including biotin, folic acid, niacin, pantothenic acid, pyridoxine, riboflavin, and thiamine (Ritala et al. 2017 ). Rapid advances in precision biology enable microbial programming to produce complex organic molecules (Augustin et al. 2023 ). Sugars, alcohols, organic acids, and hydrocarbons are simple organic feedstocks that can be used to culture microorganisms. In the field of carbohydrates, precision fermentation for the production of oligosaccharides has received the most attention. Several patents describe the construction of genetically engineered microbial cells to enhance oligosaccharide production. The primary targets are human milk and its associated oligosaccharides applied to infant formula and supplements. These oligosaccharides provide non-nutritional biological properties to infants, such as promoting gut health and the growth of beneficial microflora in the gut (Ambrogi et al. 2023 ; Barile and Rastall 2013 ). Microbial biomass producers often prefer low-cost organic by-products from the food industry, such as molasses, vegetable starch, and whey (Linder 2019 ). Microbial biomass production costs are also strongly influenced by choice of organic substrate for microbial growth (often called feedstock) (Linder 2019 ). The use of fermentation has been a useful method of food preservation in the past. the microbial populations involved made the resulting products typical concerning where processing occurred (Campbell-Platt 1994 ).

Large-scale production of fermented food products involves the use of starter cultures. defined aliquots of selected microbial cultures are added to the substrate to be fermented. depending on the selected starter culture, the fermentation process can be directed. for example, lactic acid bacteria (LAB) ferment lactose present in the substrate by lowering the pH; they inhibit the growth of undesirable bacteria but also contribute to the flavor and texture of the food (Parente et al. 2017 ). There are still inherent risks, especially when using traditional or spontaneous fermentation. Pathogenic microorganisms or harmful metabolites can spoil the final product and pose a health risk to consumers. Therefore, applying genomic analysis will help improve safety through the early detection of harmful microorganisms. Finally, combining genomics and synthetic biology to design desirable traits rationally holds promise for using non-food biomass to create new foods that are safe, healthy, and appealing to consumers (Teng et al. 2021 ). Genomic studies of food microbiomes have made great strides as rapid advances in sequencing technologies have greatly reduced sequencing costs and led to an increasing number of genomes published in public databases. Metagenomic analysis using HTS helps to reveal metabolic functions and parameters that affect fermentation processes, such as B. Substrate consumption, enzyme production, or metabolic output. Metabolic modeling combined with flux balance analysis to simulate microbial growth and metabolite production in response to changes in the culture environment (Alkema et al. 2016 ). Altogether, metabolic analysis and modeling would not only help to improve yield, taste, or texture in industrial-scale fermentation based on starter cultures but could also benefit smaller, artisanal producers to avoid contamination or spoilage by suppressing the growth of unwanted microbes or metabolic functions(Teng et al. 2021 ) By pushing the limits of precision fermentation; we can envision future food production systems in which fermentation plays a central role in producing a variety of food products.

In precision fermentation, microorganisms are programmed using synthetic biology techniques to produce food and pharmaceutical ingredients as cell factories (Pham 2018 ). Selection of recombinant host microorganisms and strain engineering is the first task to determine the possibility of constructing a microorganism that expresses and produces target molecules in sufficient quantities using appropriate fermentation conditions to increase production efficiency. Microbial hosts are preferred because they are easily manipulated genetically, and standardized fermentation equipment can be used. For food applications, strain engineering often utilizes benign bacteria (e.g., Bacillus spp.) and yeasts because microorganisms that are generally considered safe (GRAS) or harmless are preferred for food applications and so strain engineering often utilizes benign bacteria (such as Bacillus spp.), yeasts (such as  Saccharomyces cerevisiae, Pichia pastoris  (now  Komagataella phaffii ), Kluyveromyces spp.), or filamentous fungi (such as Trichoderma spp., notably the popular  T. reesei  strains) (Chai et al. 2022a , b ).

Innovation can occur through novel species and strains or by leveraging genetic engineering and synthetic biology techniques to optimize the yield of desired products, for example, by improving expression, secretion, substrate conversion, and product titer. The untapped potential of natural microbial biodiversity to provide efficient microbial cell factories for novel and safe fermented foods is revealed by “omics” tools and recent advances in synthetic biology. These tools can be utilized to develop products that match desired characteristics and precisely control the fermentation process rather than randomly (Teng et al. 2021 ). Precision fermentation is easily suited for producing selected proteins, lipids, and carbohydrates due to its ability to produce molecules that mimic comparable compositions derived from conventional agriculture. For example, the oleaginous red yeast  Rhodosporidium toruloideshas  has been genetically engineered to improve the natural synthesis of lipids, carotenoids, and novel compounds of industrial importance. A thorough understanding of the metabolism of microbial communities can also facilitate the development of new substrates, especially by-products and wastes of the food industry, for the production of value-added products. The research team has demonstrated the value of fermenting food waste with the probiotic  Bacillus subtilis  to create new foods with higher nutritional value (Mok et al. 2019 ). A more sustainable strategy is biomass fermentation for protein production, based on the ability of microorganisms to reproduce rapidly under optimal conditions and produce favorably high protein contents exceeding 50% dry weight. Examples of such products are Marmite made from yeast extract, fermented bean paste, and fungal protein from the filamentous fungus  Fusarium venenatum , which has recently been used as a raw material for artificial meat (Berka et al. 2004 ).

From a genomics point of view, single-cell protein production could be comparatively easily explored by high-throughput strain screening, adaptation, and engineering to engineering microbial strains and cell factories for protein production (Teng et al. 2021 ) Fungi are eukaryotic and saprophytic microorganisms with solid environmental adaptability, making them suitable microbial hosts for precision fermentation. The natural tendency of many fungal species to accumulate high levels of commercially valuable food compounds (organic acids, carotenoids, polyketides, and fungal pigments) makes them conveniently efficient hosts for the industrial-scale production of these products. From a metabolic engineering perspective, a key strength of using fungi compared to bacteria is that their eukaryotic nature makes them tolerant and able to functionally express heterologous eukaryotic proteins and enzymes, achieving proper protein folding and post-translational modifications (Lyu et al. 2019 ). Many species of fungi are involved in food production, such as  Saccharomyces cerevisiae  whose genome has been sequenced and allowed to produce vanillin and other aromatic compounds (Nxumalo and Thimiri Govinda Raj 2020 ). Another fungus used in precision fermentation is  Yarrowia lipolytica , a ubiquitous oleaginous fungus that tolerates wide variations in pH and salinity (Miller and Alper 2019 ). it has the unique metabolic ability to degrade hydrophobic and lipophilic substrates and accumulate more than 40 percent lipid by dry cell weight. It is an excellent source of lipid derivatives or fatty acids (Bilal et al. 2021 ). Other fungi, besides those mentioned above, can also produce valuable compounds.  Kluyveromyces lactisin  particular, is an established commercial lactase producer, and its commercial production of recombinant bovine chymosin could be considered a pioneering success in precision fermentation. Fungi play a significant role in traditional fermentations, including beer, wine, bread, cheese, sauces, vegetables, and meat.

In contrast to precision fermentation, most commercial traditional food fermentations are artisanal, natural, and largely undefined, as exemplified by the imprecise method of backing. In recent years, however, precise methods are increasingly being explored and applied to traditional fermentations to speed up the process, increase product yields, improve food quality, safety, nutrition, and flavor profiles, and reduce process costs. Such methods include high-throughput screening strategies, CRISPR-Cas9 genome editing tools, and multi-omics (Chai et al. 2022a , b ).

Valorization of food waste by fermentation

Food waste (FW) comprises complex carbohydrates, proteins, lipids, organic acids, enzymes, and nutraceuticals (Carmona-Cabello et al. 2018 ; O’Connor et al. 2021 ; Ravindran and Jaiswal 2016 ). Although its definition has been widely debated, according to the Food and Agriculture Organization (FAO), it is defined as the “total occurred qualitative and quantitative food losses during the supply chain process, which happens at the different stages like production, post-harvesting and processing”. FW is usually considered a non-dangerous waste, except for animal-derived waste strictly controlled by the European regulation (EC) No 1069/2009. FW is becoming a growing and vital problem locally and globally. In fact, according to the FAO, one-third of all food production is lost or wasted globally every year. FW is traditionally disposed of in landfills or incinerated for energy production (Melikoglu et al. 2013 ). The disposal of FW in landfills is related to several adverse environmental effects (Pires et al. 2021 ).

In addition, FW is responsible for more than 20% of the total global production of greenhouse gases (GHC), including methane (CH 4 ), nitrous oxide (N 2 O), and carbon dioxide (CO 2 ) (Munesue et al. 2015 ). For this reason, the prevention of its products, together with its valorization, is of crucial importance. Indeed, due to the growing public awareness of the indiscriminate disposal of FW and its harmful ecological impact, there is an increasing interest in the recycling and bioconversion of FW, and for this, FW valorization is becoming an expanding industry. Valorization of FW refers to the processes for converting food waste materials into a range of more valuable products. The recycling and the bioconversion of FW significant opportunities to support sustainable development (Capson-Tojo et al. 2016 ). Fermentation is one of the oldest approaches used for product transformation into value-added products using microorganisms. In fact, by converting these by-products through the microbial fermentation process, different value-added products can be produced, including feed and food additives, single-cell protein (SPC), biofertilizers, bioplastics, chemicals, fuels, food grade pigments and nutraceuticals (Lin et al. 2019 ). Moreover, FW valorization will bring economic, environmental, and social benefits through, in addition to the manufacture of value-added products, the mitigation of environmental pollution, and overcoming the issues related to odor and the spread of pathogens (Bilo et al. 2018 ).

Intending to valorize food waste, several promising technologies using acidogenic fermentation (Fig.  5 ) with anaerobic microbial communities are taking hold to generate different value-added products from biowastes (Ortiz-Sanchez et al. 2023 ). These techniques are often alternative or supplementary to more conventional ones and employ anaerobic digestion (Palacios et al. 2017 ). The transformation of bioproducts via natural processes is one of the significant advantages. The resulting products are safe and healthy for human consumption (Pires et al. 2021 ). Several are the products that can be recovered from FW. For instance, the carbohydrates in the FW can be fermented to produce lactic acid, ethanol, volatile fatty acids (carboxylic acids with 1 to 4 carbon atoms, VFA), or hydrogen (De Groof et al. 2021 ; Im et al. 2020 ; Tang et al. 2017 ; Zhang et al. 2021 ) and these products can be then extracted to serve as renewable commodity chemicals or liquid fuels (Kannengiesser et al. 2016 ). Moreover, to mitigate the negative impact, an enhanced approach to the waste management of the fruits and vegetables processing industry is a critical step in the transition to the bioeconomy. It is now well known that agro-industrial activity creates multiple and different types of waste, which are susceptible to being spontaneously fermented by the microbiota present, of course, in these by-products (Sabater et al. 2020 ; Valenti et al. 2020 ).

Valorization of food waste by fermentation. “Created with BioRender.com”

Many studies dealing with the fermentation of fruits and vegetable by-products as an alternative way of valorizing food waste using different microorganisms have been reported in the literature (Lu et al. 2022 ). Several examples are reported in the literature based on fermentation-based valorization strategies, including the anaerobic digestion of organic feedstock, date palm waste, cocoa by-products, and sourdough to produce lactic acid as an alternative for raw material, enzymes, polysaccharides, beverages, and nutraceuticals (Vasquez et al. 2019 ). The bacteria commonly used in controlled food manufacture are  Streptococcus thermophilus ,  Lactococcus lactis ,  Leuconostoc  spp., and  Lactobacillus  spp., for dairy products and the genera  Pediococcus,   Oenococcus , and  Weissella  play a pivotal role in plant-based fermented products (Bachtarzi et al. 2019 ). These valorization strategies using these bacteria, which we can also refer to as lactic acid bacteria (LAB), counted the production of lactic acid that could be replenished in the food chain, as well as improving the digestibility of proteins and the sensory properties of these plant by-products that could be used for food ingredients. However, fermentation strategies and bioconversion processes have been described to increase digestibility, enhance nutritional value and decrease the levels of antinutritional factors in these substrates, also employing other bacterial species, yeast, and molds (Yue et al. 2014 ). Therefore, the fermentation of agro-feed residues by LAB, alone or in combination with other microorganisms, paves the way for developing new sustainable circular economy strategies. In addition to fermentation strategies using LAB, other fermentative bacteria are reported to have been applied to valorize vegetable by-products (Table 11 ) and other vegetable sources, including different Clostridium and Bacillus bacterial species. Most of these applications focused on producing functional ingredients, such as lactic acid, poly-γ-glutamic acid, bioactive peptides to be reintegrated into the food chain, and other compounds like glycosidases or caproate of industrial interest. Regarding the genus Bacillus ,  Bacillus coagulans ,  Bacillus amyloliquefaciens ,  Bacillus licheniformis  and  B. subtilis  have been used, alone or in combination with other bacterial species and with fungi, to ferment products derived from rice, soy, oak, fruit, sorghum (Tropea 2022 ). On the other hand, it should be noted that the Clostridium bacterial species is mainly used in the fermentation fruit waste. For example, in this regard, a successful fermentation strategy has been reported using both  Clostridium cellulovorans  and  Clostridium beijerinckii  strains to ferment mandarin orange waste. In this study, it has been demonstrated that, although normally, D-limonene included in citrus fruits inhibits yeast activity and makes ethanolic fermentation difficult; however, the physiological concentration of D-limonene does not inhibit the growth of the two Clostridium strains. Thus, starting from the isopropanol-butanol-ethanol fermenting ability of  C. beijerinckii  and the cellulosic biomass-degrading capacity of  C. cellulovorans  allows biofuels to be produced from this particular specific fruit waste (Yalemtesfa and Tenkegna 2010 ). Moreover, it has been highlighted the possibility of using vegetable and fruit waste to generate bioenergy in the form of biofuel. Fruit wastes, in particular, were used in the production of bioethanol. Instead, vegetable wastes, high in cellulose, hemicelluloses, and lignin, were employed to produce second-generation bioethanol (Thi et al. 2016 ). Moreover, Soya by-products were mostly subjected to solid-state fermentation at 30–47 °C using  Aspergillus niger  and  Bacillus  species or yeast employing lower temperatures (20–28 °C) (Wang et al. 2019 ). Instead, Barley bran and brewing waste were mostly inoculated with  Aspergillus Trichoderma  and LAB species. Another example of the use of fermentation to valorize FW is reported by Brancoli et al. ( 2021 ). The authors reported a solid-state fermentation process carried out by the edible fungus Neurospora intermedia using bread waste as feedstock for producing a protein-rich food product. In this research, which can contribute to highlighting how it is possible to manage wasted bread more sustainably, it has been proposed that solid-state fermentation could be used to recover the otherwise discarded surplus bread (Brancoli et al. 2021 ; Tropea 2022 ). Another opportunity is the possibility of using food industry waste as animal feed. This possibility appears to be very interesting, as it would bring both environmental and public benefits besides reducing animal production costs. As reported by Tropea et al. (Tropea et al. 2021 ), among the microbial cultures used in the biotechnological methods to recover food waste, lactic bacteria have several advantages over other bacterial species, especially in animal/fish processing wastes. They are, in fact, generally recognized as safe (GRAS).

Moreover, it has been shown that the products obtained upon the fermentation with  Lactobacillus  are also reported to have other beneficial effects on aquatic animal intestines, such as antimicrobial and antioxidative properties (Hoseinifar et al. 2014 ). Fermented fish waste appears as a liquid product, obtained from the liquefaction of tissues carried out by the enzymes already present in the fish and expedited by an acid pH (Tropea et al. 2021 ). It has been observed that these fish-derived products can rapidly adapt to the intestines of both aquatic and domestic animals, thus making it possible for them to be used in probiotic aquaculture feeds. For instance, studies are reported in the literature in which fish by-products (non-edible parts such as head, viscera, skin, and bones) of  Dicentrarchus labrax  are fermented by the microorganisms  S. cerevisiae  strains and  Lactobacillus reuteri  strains (Tropea et al. 2021 ). It has also been shown a fermentation process using non-sterilized fish wastes, supplemented with lemon peel as a filler and prebiotic source, carried on by two combined starter cultures of  Saccharomyces cerevisiae  and  Lactobacillus reuteri . In this process, fish waster was bio-converted into a high protein content supplement used for aquaculture feeds. The final fermented product was found to be poor in spoilage microorganisms and rich in healthy microorganisms by displaying a lipid and protein content that makes it suitable for aquaculture feed. These results encourage fish waste and lemon peel conversion into animal feed (Tropea et al. 2021 ). Munesue et al. ( 2015 ) showed another use of food waste valorization through fermentation. Their study used pomaces, i.e., the waste generated from pressing fruits and olives to obtain juices and olive oil, as a feed supplement for animal production. The authors reported that the food obtained from animals fed with fermented pomaces was free from negative effects and with an improvement in nutritional quality.

Fermentation processes for valorizing food waste can also be an attractive opportunity to obtain new value-added products in other fields besides food, such as the cosmetic and pharmaceutical fields. A study conducted by Ferracane et al. ( 2021 ) was intended to evaluate the production and characteristics of soaps made from non-edible fermented olive oil (NEFOO soap) by assessing the pH, color, and solubility. Moreover, the glucan and pectin contents found in the green husks of walnuts grown in two different soil and climate areas of Southern Italy were also evaluated for their potential use after fermentation in food, cosmetic, and pharmaceuticals fields in a study carried out by La Torre et al. (La Torre et al. 2020 ). To date, few studies focus on the possibility of producing biogas from fermented FW. This biogas could then be used for heat or electricity production. In particular, there are several biotechnological processes, like one or two-stage fermentation, dark fermentation combined with aerobic digestion, and photo fermentation combined with aerobic digestion, which can be used to convert the plenty of organic fraction present in the FW to hydrogen. A study has shown that the higher the carbohydrate content of food waste, the better it will be valorized and converted into H 2 . Studies also show that food waste is suitable for methane production thanks to its physical and chemical characteristics (Thi et al. 2016 ). Finally, Panyawoot et al. ( 2022 ) conducted a study to evaluate the effects of the feed obtained via fermentation on final consumers. In this study, the authors assessed the impact of fermented discarded durian peel with  Lactobacillus casei , cellulase, and molasses alone or combined in total mixed rations on feed utilization, digestibility, ruminal fermentation, and nitrogen utilization in growing crossbreed Thai Native-Anglo-Nubians goats. The research highlighted that the discarded durian peel fermented with molasses and  L. casei  had a much more excellent digestibility and propionate concentration. On the other hand, this product led to less methane and urinary nitrogen production.

A future perspective on fermentation

Fermentation methods have produced many products for many years, including chemicals, materials, food, and medicines. In general, and excluding medicines, industrials fermentations are less competitive compared to the chemical industries or agriculture. More and more products can be obtained by fermentation through a safe, green, and sustainable process. However, for this technology to be increasingly competitive in the future, some issues must be solved. Some of them are freshwater shortage, heavy energy consumption, microbial contamination, the complexity of sterile operations, poor oxygen utilization in the cultures, food-related ingredients as substrates et al. For these reasons, future fermentation processes should be more effective and better from the point of view of the issues just mentioned (Chen and Jiang 2018 ). First, new fermentation methodologies should avoid the problems of bacterial contamination. Indeed, the microorganisms currently used are very susceptible to contamination by other microorganisms. For example, bacterial strains commonly used for fermentation methods, such as  E. coli  and  Bacillus  spp.,  Corynebacterium glutamicum , and  Pseudomonas  spp., and also yeast is grown in mild conditions, which also allow the growth of most microorganisms present in the air, in the water or the soil (Chen and Jiang 2018 ). For this, production facilities must be sterilized entirely to prevent microbiological contamination. This makes processes extremely complex, which also impacts the cost of production, which becomes higher. Therefore, the use of more resistant microorganisms and the implementation of measures to prevent contamination are two main requirements for the future improvement of fermentation processes. A study conducted on two bacteria  Halomonas  spp. and  Xerophiles  demonstrated that using these bacterial strains could answer the challenge of bacterial contamination. These microorganisms, extremophilic or unique substrate-selected bacteria, can grow under conditions that, at the same time, prevent the development of other microorganisms. As a result, since sterilization can be avoided, fermentation procedures can be more straightforward, and the presence of highly trained microbial fermentation engineers may be avoided.

Moreover, as these extremophile bacteria are more robust, they are also more stable under changing growth conditions, allowing the automation of the procedures (Chen and Jiang 2018 ). In future fermentation techniques, the problem of freshwater shortage could be solved by recycling the fermentation broth or using seawater rather than fresh water. The fermentation broth is rich in substances such as quorum-sensing molecules, proteins, polysaccharides, genetic materials, and lipids that could be used in cellular metabolic processes and thus become nutrients for the cells still (Yue et al. 2014 ). Another step in the prospects of fermentation processes will be favoring anaerobic or microaerobic microorganisms. Indeed, today’s fermentation processes use aerobic bacteria that need a lot of oxygen to grow and to convert substrates into products, especially in large-scale bioreactors, in which air compressors provide oxygen. However, since oxygen solubility in water is low, most of these molecules escape into the air, passing through the bioreactors. One solution adopted is the overexpression of bacterial hemoglobin to improve the oxygen uptake, but the use of anaerobic/microaerophilic bacteria would really help and would also minimize energy consumption, especially during product formation. Furthermore, using microorganisms growing in a wide range of temperatures will save even more energy (Ouyang et al. 2018 ).

Currently, glucose derived from hydrolysate starch is mainly used to produce several products. In future fermentation, waste substrates, such as molasses, activated sludge, cellulose, hydrolyzed sugars, methane, CO, and H 2 , should be used as nutrients for cellular growth, avoiding waste production. Future fermentation will rely on modifying and controlling bacterial cell morphology and self-aggregation cell ability to more simply separate cells and fermented broth only by gravity, thus without using centrifugation and filtration techniques. These two expensive and time-consuming methods are currently used to separate smaller cells and heavily fermented broth (Wang et al. 2019 ). Fermentation industries also create a lot of waste water composed mainly of organic cell debris and inorganic salts. Waste products could be treated to become nutritive molecules for the cell to grow again. In this way, the treated fermented broth could return to the bioreactors as food for cell growth and avoid wastewater generation (Tang et al. 2017 ). Moreover, new fermentation approaches will focus on using bacteria resistant to extreme conditions. For instance, it was reported that the bacterium  Halomonas campaniensis  sp. LS21 was able under non-sterilization conditions continuously for several days without contamination (Yue et al. 2014 ). Most of the current fermentation processes are run batch or fed-batch and require a lot of heavy manual controls (Chen and Jiang 2018 ).

Moreover, using plastic materials will reduce bioreactors’ weight and enhance structures’ transparency. Using cement instead will allow the building of larger bioreactors like building skyscrapers. Future fermentations will be conducted under sterilization conditions. The fact that future fermentations will be done under non-sterile and in continuous conditions controlled by artificial intelligence (AI) will reduce even more water and energy consumption (Chen and Liu 2021 ). All fermentation processes generate supernatants and solid biomass as wastes. Both these two products need to be treated. For this, future fermentations can be designed to produce small molecular extracellular products and insoluble intracellular inclusion bodies, i.e., polyhydroxyalkanoates (PHA), polyphosphates, and so on. In this way, there would be a more significant recovery of products, otherwise eliminated, starting from a single process, improving the process economy (Ma et al. 2020 ).

The scientific investigations have provided deep insight into fermentation technology’s benefits regarding human health, food properties, and ecological well-being. Intriguingly, fermented functional foods have emerged as a critical subsector of the functional food industry, which has grown steadily over the past few years. Using various microbial species, particularly yeasts and various LAB strains, has significant industrial uses and even more promising future benefits in developing healthy cultured food and beverages. Fermentation has many potential health benefits, including producing beneficial lactic acid bacteria, ease of metabolism, increased nutritional availability, improved state of mind and behavior, and cardiovascular health benefits. Dairy and meat are the most popular fermented products widely consumed. On the other side, along with dairy and meat, fermented fruit and vegetables are well known for their worldwide consumption and health benefits. Increased awareness of alternative proteins has recently expanded fermented products with core ingredients of insects and seaweed. Moreover, to maximize the bioconversion efficiency of food waste, it is necessary to optimize the food-derived waste and use cutting-edge biotechnology methods. Innovative techniques like precision fermentation are well-suited to manufacture desired proteins, lipids, and carbohydrates because they enable the generation of molecules with similar constitutions as their conventionally farmed counterparts. In the future, fermentation industries will operate continuously, automation can be installed, and this will lead to a reduction in human involvement and the prevention of mistakes. In future fermentation, low-cost materials such as plastics, cement, or ceramic can be used instead of steel. In the bargain, Artificial Intelligence will be in charge of controlling fermentation, thus providing more efficient, sterile, and less energy, water, and workforce processes.

Data availability

The data that support the findings of this study are available from the corresponding author, [Shahida Anusha Siddiqui], upon reasonable request.

Achi OK, Asamudo NU (2019) Cereal-based fermented foods of africa as functional foods. In: Mérillon JM, Ramawat K (eds) Bioactive molecules in food. Reference series in phytochemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-78030-6_31

Chapter   Google Scholar  

Adams MR (1998) Fermented weaning foods. In: Wood BJB (ed) Microbiology of Fermented Foods. Springer, Boston. https://doi.org/10.1007/978-1-4613-0309-1_25

Adebo OA (2020) African sorghum-based fermented foods: past. Curr Future Prospects Nutr 12:1111. https://doi.org/10.3390/nu12041111

Article   CAS   Google Scholar  

Adebo OA, Njobeh PB, Sidu S, Adebiyi JA, Mavumengwana V (2017) Aflatoxin B1 degradation by culture and lysate of a Pontibacter specie. Food Control 80:99–103. https://doi.org/10.1016/j.foodcont.2017.04.042

Adebo OA, Njobeh PB, Adeboye AS, Adebiyi JA, Sobowale SS, Ogundele OM, Kayitesi E (2018) Innovations in technologies for fermented food and beverage ındustries. In: Panda S, Shetty P (eds) Food microbiology and food safety. Springer, Cham. https://doi.org/10.1007/978-3-319-74820-7_4

Adesulu AT, Awojobi KO (2014) Enhancing sustainable development through indigenous fermented food products in Nigeria. Afr J Microbiol Res 8(12):1338–1343. https://doi.org/10.5897/ajmr2013.5439

Article   Google Scholar  

Adunphatcharaphon S, Petchkongkaew A, Visessanguan W (2021) In vitro mechanism assessment of zearalenone removal by plant-derived Lactobacillus plantarum BCC 47723. Toxins 13(4):286. https://doi.org/10.3390/toxins13040286

Article   CAS   PubMed   PubMed Central   Google Scholar  

Afzaal M, Saeed F, Anjum F, Waris N, Husaain M, Ikram A, Ateeq H, Muhammad Anjum F, Suleria H (2021) Nutritional and ethnomedicinal scenario of koumiss: a concurrent review. Food Sci Nutr 9(11):6421–6428. https://doi.org/10.1002/fsn3.2595

Ahnan-Winarno AD, Cordeiro L, Winarno FG, Gibbons J, Xiao H (2021) Tempeh: a semicentennial review on its health benefits, fermentation, safety, processing, sustainability, and affordability. Compr Rev Food Sci Food Saf 20(2):1717–1767. https://doi.org/10.1111/1541-4337.12710

Article   CAS   PubMed   Google Scholar  

Akbar A, Sadiq MB, Ali I, Anwar M, Muhammad N, Muhammad J, Shafee M, Ullah S, Gul Z, Qasim S, Ahmad S, Anal AK (2019) Lactococcus lactis subsp. lactis isolated from fermented milk products and its antimicrobial potential. CyTA J Food 17(1):214–220. https://doi.org/10.1080/19476337.2019.1575474

Alapont C, López-Mendoza MC, Gil JV, Martínez-Culebras PV (2014) Mycobiota and toxigenic Penicillium species on two Spanish dry-cured ham manufacturing plants. Food Addit Contam Part A 31(1):93–104. https://doi.org/10.1080/19440049.2013.849007

Alessandria V, Rantsiou K, Dolci P, Cocolin L (2014) Methodologies for the study of microbial ecology in fermented sausages. In: Toldrá F, Hui YH, Astiasarán I, Sebranek JG, Talon R (eds) Handbook of fermented meat and poultry. Wiley, pp 177–188. https://doi.org/10.1002/9781118522653.ch21

Algonaiman R, Alharbi HF, Barakat H (2022) Antidiabetic and hypolipidemic efficiency of Lactobacillus plantarum fermented oat ( Avena sativa ) extract in streptozotocin-induced diabetes in rats. Fermentation 8(6):267. https://doi.org/10.3390/fermentation8060267

Alkema W, Boekhorst J, Wels M, van Hijum SAFT (2016) Microbial bioinformatics for food safety and production. Brief Bioinform 17(2):283–292. https://doi.org/10.1093/bib/bbv034

Al-Mohammadi A-R, Ibrahim RA, Moustafa AH, Ismaiel AA, Abou Zeid A, Enan G (2021) Chemical constitution and antimicrobial activity of kefir fermented beverage. Molecules 26(9):2635. https://doi.org/10.3390/molecules26092635

Alves SP, Alfaia CM, Škrbić BD, Živančev JR, Fernandes MJ, Bessa RJB, Fraqueza MJ (2017) Screening chemical hazards of dry fermented sausages from distinct origins: Biogenic amines, polycyclic aromatic hydrocarbons and heavy elements. J Food Compos Anal 59:124–131. https://doi.org/10.1016/j.jfca.2017.02.020

Ambrogi V, Bottacini F, Cao L, Kuipers B, Schoterman M, van Sinderen D (2023) Galacto-oligosaccharides as infant prebiotics: production, application, bioactive activities and future perspectives. Crit Rev Food Sci Nutr 63(6):753–766. https://doi.org/10.1080/10408398.2021.1953437

Angeles-Agdeppa I, Sun Y, Tanda KV (2020) Dietary pattern and nutrient intakes in association with non-communicable disease risk factors among Filipino adults: a cross-sectional study. Nutr J 19(1):79. https://doi.org/10.1186/s12937-020-00597-x

Anggraini, H., Tongkhao, K., and Chanput, W. 2018. Reducing milk allergenicity of cow, buffalo, and goat milk using lactic acid bacteria fermentation. 070010. https://doi.org/10.1063/1.5062808

Antone U, Ciprovica I, Zolovs M, Scerbaka R, Liepins J (2022) Propionic acid fermentation-study of substrates, strains, and antimicrobial properties. Fermentation 9(1):26. https://doi.org/10.3390/fermentation9010026

Anusha Siddiqui S, Bahmid NA, Mahmud CMM, Boukid F, Lamri M, Gagaoua M (2022) Consumer acceptability of plant-, seaweed-, and insect-based foods as alternatives to meat: a critical compilation of a decade of research. Crit Rev Food Sci Nutr. https://doi.org/10.1080/10408398.2022.2036096

Article   PubMed   Google Scholar  

Apriyantono A, Wiratma E, Nurhayati HH, Lie L, Judoamidjojo M, Puspitasari-Nienaber NL, Budiyanto S, Sumaryanto H (1996) Analysis of volatiles of Kecap Manis (a typical ındonesian soy sauce). Flav Sci. https://doi.org/10.1533/9781845698232.1.62

Asama T, Kimura Y, Kono T, Tatefuji T, Hashimoto K, Benno Y (2016) Effects of heat-killed Lactobacillus kunkeei YB38 on human intestinal environment and bowel movement: a pilot study. Benef Microb 7(3):337–344. https://doi.org/10.3920/BM2015.0132

Ashokkumar V, Flora G, Venkatkarthick R, SenthilKannan K, Kuppam C, Mary Stephy G, Kamyab H, Chen W-H, Thomas J, Ngamcharussrivichai C (2022) Advanced technologies on the sustainable approaches for conversion of organic waste to valuable bioproducts: emerging circular bioeconomy perspective. Fuel 324:124313. https://doi.org/10.1016/j.fuel.2022.124313

Augustin MA, Hartley CJ, Maloney G, Tyndall S (2023) Innovation in precision fermentation for food ingredients. Crit Rev Food Sci Nutr. https://doi.org/10.1080/10408398.2023.2166014

Austin-Watson C, Grant A, Brice M (2013) Suppression of Listeria monocytogenes by the native micro-flora in teewurst sausage. Foods 2(4):478–487. https://doi.org/10.3390/foods2040478

Azizkhani M, Saris PEJ, Baniasadi M (2021) An in-vitro assessment of antifungal and antibacterial activity of cow, camel, ewe, and goat milk kefir and probiotic yogurt. J Food Meas Charact 15(1):406–415. https://doi.org/10.1007/s11694-020-00645-4

Bachmann H, Pronk JT, Kleerebezem M, Teusink B (2015) Evolutionary engineering to enhance starter culture performance in food fermentations. Curr Opin Biotechnol 32:1–7. https://doi.org/10.1016/j.copbio.2014.09.003

Bachtarzi N, Kharroub K, Ruas-Madiedo P (2019) Exopolysaccharide-producing lactic acid bacteria isolated from traditional Algerian dairy products and their application for skim-milk fermentations. LWT 107:117–124. https://doi.org/10.1016/j.lwt.2019.03.005

Bala JD, Kuta FA, Abioye OP, Adabara NU, Adelere IA, Abdulsalam R, Al-Gheethi AAS, Kaizar H, Onovughakpor C (2017) Microbiology and quality assessment of burukutu: a Nigerian fermented alcoholic beverage. Niger J Technol Res 12(1):103–108. https://doi.org/10.4314/njtr.v12i1.15

Baldin JC, Munekata PES, Michelin EC, Polizer YJ, Silva PM, Canan TM, Pires MA, Godoy SHS, Fávaro-Trindade CS, Lima CG, Fernandes AM, Trindade MA (2018) Effect of microencapsulated Jabuticaba ( Myrciaria cauliflora ) extract on quality and storage stability of mortadella sausage. Food Res Int 108:551–557. https://doi.org/10.1016/j.foodres.2018.03.076

Barile D, Rastall RA (2013) Human milk and related oligosaccharides as prebiotics. Curr Opin Biotechnol 24(2):214–219. https://doi.org/10.1016/j.copbio.2013.01.008

Barni S, Liccioli G, Sarti L, Giovannini M, Novembre E, Mori F (2020) Immunoglobulin E (IgE)-mediated food allergy in children: epidemiology, pathogenesis, diagnosis, prevention, and management. Medicina 56(3):111. https://doi.org/10.3390/medicina56030111

Article   PubMed   PubMed Central   Google Scholar  

Bartkiene E, Zokaityte E, Starkute V, Zokaityte G, Kaminskaite A, Mockus E, Klupsaite D, Cernauskas D, Rocha JM, Özogul F, Guiné RPF (2023) Crickets ( Acheta domesticus ) as wheat bread ingredient: influence on bread quality and safety characteristics. Foods 12(2):325. https://doi.org/10.3390/FOODS12020325/S1

Bastidas-Oyanedel J-R, Bonk F, Thomsen MH, Schmidt JE (2015) Dark fermentation biorefinery in the present and future (bio)chemical industry. Rev Environ Sci Bio/technol 14(3):473–498. https://doi.org/10.1007/s11157-015-9369-3

Bengoa AA, Iraporda C, Garrote GL, Abraham AG (2019) Kefir micro-organisms: their role in grain assembly and health properties of fermented milk. J Appl Microbiol 126(3):686–700. https://doi.org/10.1111/jam.14107

Berka RM, Nelson BA, Zaretsky EJ, Yoder WT, Rey MW (2004) Genomics of Fusarium venenatum : An alternative fungal host for making enzymes. Appl Mycol Biotechnol 4:191–203. https://doi.org/10.1016/S1874-5334(04)80010-8

Bertuzzi T, Gualla A, Morlacchini M, Pietri A (2013) Direct and indirect contamination with ochratoxin A of ripened pork products. Food Control 34(1):79–83. https://doi.org/10.1016/j.foodcont.2013.04.011

Bhutia MO, Thapa N, Tamang JP (2021) Molecular characterization of bacteria, detection of enterotoxin genes, and screening of antibiotic susceptibility patterns in traditionally processed meat products of Sikkim, India. Front Microbiol. https://doi.org/10.3389/fmicb.2020.599606

Bilal M, Xu S, Iqbal HMN, Cheng H (2021) Yarrowia lipolytica as an emerging biotechnological chassis for functional sugars biosynthesis. Crit Rev Food Sci Nutr 61(4):535–552. https://doi.org/10.1080/10408398.2020.1739000

Bilo F, Pandini S, Sartore L, Depero LE, Gargiulo G, Bonassi A, Federici S, Bontempi E (2018) A sustainable bioplastic obtained from rice straw. J Clean Prod 200:357–368. https://doi.org/10.1016/j.jclepro.2018.07.252

Bingol EB, Ciftcioglu G, Yilmaz Eker F, Yardibi H, Yesil O, Bayrakal G, Demirel G (2014) Effect of starter cultures combinations on lipolytic activity and ripening of dry fermented sausages. Ital J Anim Sci. https://doi.org/10.4081/ijas.2014.3422

Bintsis T, Papademas P (2022) The evolution of fermented milks, from artisanal to industrial products: a critical review. Fermentation 8(12):679. https://doi.org/10.3390/fermentation8120679

Biscola V, Tulini FL, Choiset Y, Rabesona H, Ivanova I, Chobert J-M, Todorov SD, Haertlé T, Franco BDGM (2016) Proteolytic activity of Enterococcus faecalis VB63F for reduction of allergenicity of bovine milk proteins. J Dairy Sci 99(7):5144–5154. https://doi.org/10.3168/jds.2016-11036

Biscola V, Choiset Y, Rabesona H, Chobert JM, Haertlé T, Franco BDGM (2018) Brazilian artisanal ripened cheeses as sources of proteolytic lactic acid bacteria capable of reducing cow milk allergy. J Appl Microbiol 125(2):564–574. https://doi.org/10.1111/jam.13779

Borremans A, Lenaerts S, Crauwels S, Lievens B, Van Campenhout L (2018) Marination and fermentation of yellow mealworm larvae ( Tenebrio molitor ). Food Control 92:47–52. https://doi.org/10.1016/J.FOODCONT.2018.04.036

Botthoulath V, Upaichit A, Thumarat U (2018) Characterization of Listeria-active bacteriocin produced by a new strain Lactobacillus plantarum subsp. plantarum SKI19 isolated from “sai krok e-san mu.” Int Food Res J 25(6):2362–2371

CAS   Google Scholar  

Bourdichon F, Arias E, Babuchowski A, Bückle A, Bello FD, Dubois A, Fontana A, Fritz D, Kemperman R, Laulund S, McAuliffe O, Miks MH, Papademas P, Patrone V, Sharma DK, Sliwinski E, Stanton C, Von Ah U, Yao S, Morelli L (2021) The forgotten role of food cultures. FEMS Microbiol Lett. https://doi.org/10.1093/femsle/fnab085

Brancoli P, Gmoser R, Taherzadeh MJ, Bolton K (2021) The use of life cycle assessment in the support of the development of fungal food products from surplus bread. Fermentation 7(3):173. https://doi.org/10.3390/fermentation7030173

Bryant C, Sanctorum H (2021) Alternative proteins, evolving attitudes: Comparing consumer attitudes to plant-based and cultured meat in Belgium in two consecutive years. Appetite 161:105161. https://doi.org/10.1016/J.APPET.2021.105161

Bücher C, Burtscher J, Domig KJ (2021) Propionic acid bacteria in the food industry: An update on essential traits and detection methods. Compr Rev Food Sci Food Saf 20(5):4299–4323. https://doi.org/10.1111/1541-4337.12804

CAC (2003) Standard for fermented milks. https://www.fao.org/fao-who-codexalimentarius/sh-proxy/en/?lnk=1&url=https%253A%252F%252Fworkspace.fao.org%252Fsites%252Fcodex%252FStandards%252FCXS%2B243-2003%252FCXS_243e.pdf

Cai T, Wu H, Qin J, Qiao J, Yang Y, Wu Y, Qiao D, Xu H, Cao Y (2019) In vitro evaluation by PCA and AHP of potential antidiabetic properties of lactic acid bacteria isolated from traditional fermented food. LWT 115:108455. https://doi.org/10.1016/j.lwt.2019.108455

Cai YX, Augustin MA, Jegasothy H, Wang JH, Terefe NS (2020) Mild heat combined with lactic acid fermentation: a novel approach for enhancing sulforaphane yield in broccoli puree. Food Funct 11(1):779–786. https://doi.org/10.1039/c9fo02089f

Campbell-Platt G (1994) Fermented foods-a world perspective. Food Res Int 27(3):253–257. https://doi.org/10.1016/0963-9969(94)90093-0

Cao ZH, Green-Johnson JM, Buckley ND, Lin QY (2019) Bioactivity of soy-based fermented foods: a review. Biotechnol Adv 37(1):223–238. https://doi.org/10.1016/J.BIOTECHADV.2018.12.001

Caparros Megido R, Sablon L, Geuens M, Brostaux Y, Alabi T, Blecker C, Drugmand D, Haubruge É, Francis F (2014) Edible ınsects acceptance by belgian consumers: promising attitude for entomophagy development. J Sens Stud 29(1):14–20. https://doi.org/10.1111/joss.12077

Caparros Megido R, Gierts C, Blecker C, Brostaux Y, Haubruge É, Alabi T, Francis F (2016) Consumer acceptance of insect-based alternative meat products in Western countries. Food Qual Prefer 52:237–243. https://doi.org/10.1016/j.foodqual.2016.05.004

Capson-Tojo G, Rouez M, Crest M, Steyer JP, Delgenès JP, Escudié R (2016) Food waste valorization via anaerobic processes: a review. Rev Environ Sci Bio/technol 15(3):499–547. https://doi.org/10.1007/s11157-016-9405-y

Carmona-Cabello M, Garcia IL, Leiva-Candia D, Dorado MP (2018) Valorization of food waste based on its composition through the concept of biorefinery. Curr Opin Green Sustain Chem 14:67–79. https://doi.org/10.1016/j.cogsc.2018.06.011

Celotti E, Stante S, Ferraretto P, Román T, Nicolini G, Natolino A (2020) High power ultrasound treatments of red young wines: effect on anthocyanins and phenolic stability indices. Foods 9(10):10. https://doi.org/10.3390/foods9101344

Chai KF, Ng KR, Samarasiri M, Chen WN (2022a) Precision fermentation to advance fungal food fermentations. Curr Opin Food Sci 47:100881. https://doi.org/10.1016/j.cofs.2022.100881

Chai S, Zhu Z, Tian E, Xiao M, Wang Y, Zou G, Zhou Z (2022b) Building a versatile protein production platform using engineered Trichoderma reesei . ACS Synth Biol 11(1):486–496. https://doi.org/10.1021/acssynbio.1c00570

Chandrasekhar K, Venkata Mohan S (2014) Induced catabolic bio-electrohydrolysis of complex food waste by regulating external resistance for enhancing acidogenic biohydrogen production. Biores Technol 165:372–382. https://doi.org/10.1016/j.biortech.2014.02.073

Charlton S, Ramsøe A, Collins M, Craig OE, Fischer R, Alexander M, Speller CF (2019) New insights into Neolithic milk consumption through proteomic analysis of dental calculus. Archaeol Anthropol Sci 11(11):6183–6196. https://doi.org/10.1007/s12520-019-00911-7

Chaudhari DD, Singh R, Mallappa RH, Rokana N, Kaushik JK, Bajaj R, Batish VK, Grover S (2017) Evaluation of casein and whey protein hydrolysates as well as milk fermentates from Lactobacillus helveticus for expression of gut hormones. Indian J Med Res 146:409–419. https://doi.org/10.4103/ijmr.IJMR_802_15

Chen GQ, Jiang XR (2018) Next generation industrial biotechnology based on extremophilic bacteria. Curr Opin Biotechnol 50:94–100. https://doi.org/10.1016/j.copbio.2017.11.016

Chen G, Liu X (2021) On the future fermentation. Microb Biotechnol 14(1):18–21. https://doi.org/10.1111/1751-7915.13674

Cho YM, Fujita Y, Kieffer TJ (2014) Glucagon-like peptide-1: glucose homeostasis and beyond. Annu Rev Physiol 76(1):535–559. https://doi.org/10.1146/annurev-physiol-021113-170315

Cho JH, Zhao HL, Kim JS, Kim SH, Chung CH (2018) Characteristics of fermented seasoning sauces using Tenebrio molitor larvae. Innov Food Sci Emerg Technol 45:186–195. https://doi.org/10.1016/J.IFSET.2017.10.010

Cho HD, Min HJ, Won YS, Ahn HY, Cho YS, Seo K (2019) Solid state fermentation process with Aspergillus kawachii enhances the cancer-suppressive potential of silkworm larva in hepatocellular carcinoma cells. BMC Complement Altern Med 19(1):241. https://doi.org/10.1186/S12906-019-2649-7/TABLES/3

Chua LS, Abdullah FI, Lim SH (2022) Physiochemical changes and nutritional content of black garlic during fermentation. Appl Food Res 2(2):100216. https://doi.org/10.1016/J.AFRES.2022.100216

Companys J, Pedret A, Valls RM, Solà R, Pascual V (2021) Fermented dairy foods rich in probiotics and cardiometabolic risk factors: a narrative review from prospective cohort studies. Crit Rev Food Sci Nutr 61(12):1966–1975. https://doi.org/10.1080/10408398.2020.1768045

Dahiya D, Nigam PS (2022) Probiotics, prebiotics, synbiotics, and fermented foods as potential biotics in nutrition improving health via microbiome-gut-brain axis. Fermentation 8:303. https://doi.org/10.3390/fermentation8070303

Dan T, Wang D, Wu S, Jin R, Ren W, Sun T (2017) Profiles of volatile flavor compounds in milk fermented with different proportional combinations of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus . Molecules 22(10):1633. https://doi.org/10.3390/molecules22101633

Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E, Verger EO, Kayser BD, Levenez F, Chilloux J, Hoyles L, Dumas M-E, Rizkalla SW, Doré J, Cani PD, Clément K, Consortium, M.-O (2016) Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: Relationship with gut microbiome richness and ecology. Gut Microb 65(3):426–436. https://doi.org/10.1136/gutjnl-2014-308778

Dargahi N, Johnson J, Donkor O, Vasiljevic T, Apostolopoulos V (2019) Immunomodulatory effects of probiotics: can they be used to treat allergies and autoimmune diseases? Maturitas 119:25–38. https://doi.org/10.1016/j.maturitas.2018.11.002

Das RK, Brar SK, Verma M (2016) Potential use of pulp and paper solid waste for the bio-production of fumaric acid through submerged and solid state fermentation. J Clean Prod 5(112):4435–4444. https://doi.org/10.1016/j.jclepro.2015.08.108

De Castro RJS, Ohara A, Nishide TG, Bagagli MP, Gonçalves Dias FF, Sato HH (2015) A versatile system based on substrate formulation using agroindustrial wastes for protease production by Aspergillus niger under solid state fermentation. Biocatal Agric Biotechnol 4(4):678–684. https://doi.org/10.1016/j.bcab.2015.08.010

De Groof V, Coma M, Arnot T, Leak DJ, Lanham AB (2021) Selecting fermentation products for food waste valorisation with HRT and OLR as the key operational parameters. Waste Manage 127:80–89. https://doi.org/10.1016/j.wasman.2021.04.023

De Melo Pereira GV, Neto E, Soccol VT, Medeiros ABP, Woiciechowski AL, Soccol CR (2015) Conducting starter culture-controlled fermentations of coffee beans during on-farm wet processing: growth, metabolic analyses and sensorial effects. Food Res Int 75:348–356. https://doi.org/10.1016/J.FOODRES.2015.06.027

De Noronha MC, Cardoso RR, dos Santos Dalmeida CT, Vieira do Carmo MA, Azevedo L, Maltarollo VG, Júnior JIR, Eller MR, Cameron LC, Ferreira MSL, Barros FAR (2022) Black tea kombucha: Physicochemical, microbiological and comprehensive phenolic profile changes during fermentation, and antimalarial activity. Food Chem 384:132515. https://doi.org/10.1016/J.FOODCHEM.2022.132515

De Smet J, Lenaerts S, Borremans A, Scholliers J, Van Der Borght M, Van Campenhout L (2019) Stability assessment and laboratory scale fermentation of pastes produced on a pilot scale from mealworms ( Tenebrio molitor ). LWT 102:113–121. https://doi.org/10.1016/J.LWT.2018.12.017

de Vergara CMAC, Honorato TL, Maia GA, Rodrigues S (2010) Prebiotic effect of fermented cashew apple ( Anacardium occidentale L.) juice. LWT Food Sci Technol 43(1):141–145. https://doi.org/10.1016/J.LWT.2009.06.009

De Vuyst L, Leroy F (2007) Bacteriocins from lactic acid bacteria: production, purification, and food applications. Microb Physiol 13(4):194–199. https://doi.org/10.1159/000104752

Deibel RH, Wilson GD, Niven CF (1961) Microbiology of meat curing IV. A lyophilized pediococcus cerevisiae starter culture for fermented sausage. Appl Microbiol 9(3):239–243. https://doi.org/10.1128/am.9.3.239-243.1961

Desnoues E, Baldazzi V, Génard M, Mauroux J-B, Lambert P, Confolent C, Quilot-Turion B (2016) Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development. J Exp Bot 67(11):3419–3431. https://doi.org/10.1093/jxb/erw169

Di Cagno R, Surico RF, Minervini G, Rizzello CG, Lovino R, Servili M, Taticchi A, Urbani S, Gobbetti M (2011) Exploitation of sweet cherry ( Prunus avium L.) puree added of stem infusion through fermentation by selected autochthonous lactic acid bacteria. Food Microbiol 28(5):900–909. https://doi.org/10.1016/J.FM.2010.12.008

Di Cagno R, Coda R, De Angelis M, Gobbetti M (2013) Exploitation of vegetables and fruits through lactic acid fermentation. Food Microbiol 33(1):1–10. https://doi.org/10.1016/J.FM.2012.09.003

Di Cagno R, Filannino P, Cantatore V, Polo A, Celano G, Martinovic A, Cavoski I, Gobbetti M (2020) Design of potential probiotic yeast starters tailored for making a cornelian cherry ( Cornus mas L.) functional beverage. Int J Food Microbiol 323:108591. https://doi.org/10.1016/j.ijfoodmicro.2020.108591

dos Mathias TRS, de Aguiar PF, de Silva JBA, de Mello PPM, Sérvulo EFC (2017) Brewery wastes reuse for protease production by lactic acid bacteria fermentation. Food Technol Biotechnol. https://doi.org/10.17113/ftb.55.02.17.4378

Dulf FV, Vodnar DC, Socaciu C (2016) Effects of solid-state fermentation with two filamentous fungi on the total phenolic contents, flavonoids, antioxidant activities and lipid fractions of plum fruit ( Prunus domestica L.) by-products. Food Chem 209:27–36. https://doi.org/10.1016/j.foodchem.2016.04.016

Dursun D, Dalgıç AC (2016) Optimization of astaxanthin pigment bioprocessing by four different yeast species using wheat wastes. Biocatal Agric Biotechnol 7:1–6. https://doi.org/10.1016/j.bcab.2016.04.006

EFSA (2011) Scientific opinion on risk based control of biogenic amine formation in fermented foods. EFSA J. https://doi.org/10.2903/j.efsa.2011.2393

El Mecherfi K, Lupi R, Albuquerque M, De Albuquerque C, Haertlé T (2019) Gluten fermentation with selected lactic acid bacteria strains induces its proteolysis and decreases its antigenicity. Conference: Allergy, 74: (S106). https://doi.org/10.13140/RG.2.2.25651.78886

El-Mansi EMT, Nielsen J, Mousdale D, Carlson RP (2019) Fermentation microbiology and biotechnology, 4th edn. CRC Press. https://doi.org/10.1201/9780429506987

Book   Google Scholar  

Evangelista SR, da Cruz Pedrozo Miguel MG, de Souza Cordeiro C, Silva CF, Marques Pinheiro AC, Schwan RF (2014) Inoculation of starter cultures in a semi-dry coffee ( Coffea arabica ) fermentation process. Food Microbiol 44:87–95. https://doi.org/10.1016/J.FM.2014.05.013

Fang B, Sun J, Dong P, Xue C, Mao X (2017) Conversion of turbot skin wastes into valuable functional substances with an eco-friendly fermentation technology. J Clean Prod 156:367–377. https://doi.org/10.1016/j.jclepro.2017.04.055

Farag MA, Saleh HA, El Ahmady S, Elmassry MM (2022) Dissecting yogurt: the impact of milk types, probiotics, and selected additives on yogurt quality. Food Rev Intl 38:634–650. https://doi.org/10.1080/87559129.2021.1877301

Farahmand N, Ouoba LII, Naghizadeh Raeisi S, Sutherland J, Ghoddusi HB (2021) Probiotic Lactobacilli in fermented dairy products: selective detection. Enumer Identification Scheme Microorg 9(8):1600. https://doi.org/10.3390/microorganisms9081600

Fatahi A, Soleimani N, Afrough P (2021) Anticancer activity of kefir on glioblastoma cancer cell as a new treatment. Int J Food Sci 2021:1–5. https://doi.org/10.1155/2021/8180742

Fatmawati F, Sibero MT, Trianto A, Wijayanti DP, Sabdono A, Pringgenies D, Radjasa OK (2022) The influence of fermentation using marine yeast Hortaea werneckii SUCCY001 on antibacterial and antioxidant activity of Gracilaria verrucosa . Biodiversitas 23(10):5258–5266. https://doi.org/10.13057/BIODIV/D231035

Fekete Á, Givens D, Lovegrove J (2015) Casein-derived lactotripeptides reduce systolic and diastolic blood pressure in a meta-analysis of randomised clinical trials. Nutrients 7(1):659–681. https://doi.org/10.3390/nu7010659

Feng L, Xie Y, Peng C, Liu Y, Wang H (2018a) A novel antidiabetic food produced via solid-state fermentation of tartary buckwheat using L. plantarum TK9 and L. paracasei TK1501. Food Technol Biotechnol. https://doi.org/10.17113/ftb.56.03.18.5540

Feng R, Chen L, Chen K (2018b) Fermentation trip: Amazing microbes, amazing metabolisms. Ann Microbiol 68(11):Articolo 11. https://doi.org/10.1007/s13213-018-1384-5

Fernandes N, Faria AS, Carvalho L, Choupina A, Rodrigues C, Cadavez V, Gonzales-Barron U (2022) Molecular identification of lactic acid producing bacteria isolated from alheira, a traditional portuguese fermented sausage. Foods 18(1):73. https://doi.org/10.3390/Foods2022-13035

Ferracane A, Tropea A, Salafia F (2021) Production and maturation of soaps with non-edible fermented olive oil and comparison with classic olive oil soaps. Fermentation 7(4):Articolo 4. https://doi.org/10.3390/fermentation7040245

Fibri DLN, Frøst MB (2019) Consumer perception of original and modernised traditional foods of Indonesia. Appetite 133:61–69. https://doi.org/10.1016/J.APPET.2018.10.026

Filannino P, Bai Y, Di Cagno R, Gobbetti M, Gänzle MG (2015) Metabolism of phenolic compounds by Lactobacillus spp. during fermentation of cherry juice and broccoli puree. Food Microbiol 46:272–279. https://doi.org/10.1016/j.fm.2014.08.018

Fu L, Cherayil BJ, Shi H, Wang Y, Zhu Y (2019) Food processing to eliminate food allergens and development of hypoallergenic foods. Food allergy. Springer, Singapore, pp 123–146. https://doi.org/10.1007/978-981-13-6928-5_6

Fujita A, Sarkar D, Genovese MI, Shetty K (2017) Improving anti-hyperglycemic and anti-hypertensive properties of camu-camu ( Myriciaria dubia Mc. Vaugh) using lactic acid bacterial fermentation. Process Biochem 59:133–140. https://doi.org/10.1016/j.procbio.2017.05.017

Galimberti A, Bruno A, Agostinetto G, Casiraghi M, Guzzetti L, Labra M (2021) Fermented food products in the era of globalization: tradition meets biotechnology innovations. Curr Opin Biotechnol 70:36–41. https://doi.org/10.1016/j.copbio.2020.10.006

Galli V, Venturi M, Mari E, Guerrini S, Granchi L (2022) Selection of yeast and lactic acid bacteria strains, isolated from spontaneous raw milk fermentation, for the production of a potential probiotic fermented milk. Fermentation 8(8):407. https://doi.org/10.3390/fermentation8080407

Gamba RR, Caro CA, Martínez OL, Moretti AF, Giannuzzi L, De Antoni GL, León Peláez A (2016) Antifungal effect of kefir fermented milk and shelf life improvement of corn arepas. Int J Food Microbiol 235:85–92. https://doi.org/10.1016/j.ijfoodmicro.2016.06.038

Gänzle M (2022) The periodic table of fermented foods: limitations and opportunities. Appl Microbiol Biotechnol 106(8):2815–2826. https://doi.org/10.1007/s00253-022-11909-y

Gao J, Gu F, Ruan H, Chen Q, He J, He G (2013) Induction of apoptosis of gastric cancer cells SGC7901 in vitro by a cell-free fraction of Tibetan kefir. Int Dairy J 30(1):14–18. https://doi.org/10.1016/j.idairyj.2012.11.011

García-Burgos M, Moreno-Fernández J, Alférez MJM, Díaz-Castro J, López-Aliaga I (2020) New perspectives in fermented dairy products and their health relevance. J Funct Foods 72:104059. https://doi.org/10.1016/j.jff.2020.104059

García-Cano I, Rocha-Mendoza D, Ortega-Anaya J, Wang K, Kosmerl E, Jiménez-Flores R (2019) Lactic acid bacteria isolated from dairy products as potential producers of lipolytic, proteolytic and antibacterial proteins. Appl Microbiol Biotechnol 103(13):5243–5257. https://doi.org/10.1007/s00253-019-09844-6

Gavahian M, Manyatsi TS, Morata A, Tiwari BK (2022) Ultrasound-assisted production of alcoholic beverages: from fermentation and sterilization to extraction and aging. Compr Rev Food Sci Food Saf 21(6):5243–5271. https://doi.org/10.1111/1541-4337.13043

Gernah DI, Ariahu CC, Ingbian IK (2011) Effects of malting and lactic fermentation on some chemical and functional properties of maize ( Zea mays ). Am J Food Technol 6(5):404–412. https://doi.org/10.3923/ajft.2011.404.412

Gholamhosseinpour A, Hashemi SMB (2019) Ultrasound pretreatment of fermented milk containing probiotic Lactobacillus plantarum AF1: carbohydrate metabolism and antioxidant activity. J Food Process Eng 42(1):e12930. https://doi.org/10.1111/jfpe.12930

Giacalone D, Clausen MP, Jaeger SR (2022) Understanding barriers to consumption of plant-based foods and beverages: insights from sensory and consumer science. Curr Opin Food Sci 48:100919. https://doi.org/10.1016/J.COFS.2022.100919

Gmoser R, Sintca C, Taherzadeh MJ, Lennartsson PR (2019) Combining submerged and solid state fermentation to convert waste bread into protein and pigment using the edible filamentous fungus N. intermedia . Waste Manage 97:63–70. https://doi.org/10.1016/j.wasman.2019.07.039

González-Quijano GK, Dorantes-Alvarez L, Hernández-Sánchez H, Jaramillo-Flores ME, de Jesús Perea-Flores M, Vera-Ponce de León A, Hernández-Rodríguez C (2014) Halotolerance and survival kinetics of lactic acid bacteria isolated from Jalapeño pepper ( Capsicum annuum L.) Fermentation. J Food Sci 79(8):M1545–M1553. https://doi.org/10.1111/1750-3841.12498

Gullón B, Gagaoua M, Barba FJ, Gullón P, Zhang W, Lorenzo JM (2020) Seaweeds as promising resource of bioactive compounds: overview of novel extraction strategies and design of tailored meat products. Trends Food Sci Technol 100:1–18. https://doi.org/10.1016/J.TIFS.2020.03.039

Gullón P, Astray G, Gullón B, Franco D, Campagnol PCB, Lorenzo JM (2021) Inclusion of seaweeds as healthy approach to formulate new low-salt meat products. Curr Opin Food Sci 40:20–25. https://doi.org/10.1016/J.COFS.2020.05.005

Gupta S, Abu-Ghannam N (2011) Probiotic fermentation of plant based products: possibilities and opportunities. Crit Rev Food Sci Nutr 52(2):183–199. https://doi.org/10.1080/10408398.2010.499779

Gupta GN, Srivastava S, Khare SK, Prakash V (2014) Extremophiles: an overview of microorganism from extreme environment. Int J Agric Environ Biotechnol 7(2):371–380. https://doi.org/10.5958/2230-732X.2014.00258.7

Ha NI, Mun SK, Im SB, Jang HY, Jeong HG, Kang KY, Park KW, Seo KS, Ban SE, Kim KJ, Yee ST (2022) Changes in functionality of tenebrio molitor larvae fermented by Cordyceps militaris mycelia. Foods. https://doi.org/10.3390/FOODS11162477

Haile M, Kang WH (2019a) Antioxidant activity, total polyphenol, flavonoid and tannin contents of fermented green coffee beans with selected yeasts. Fermentation 5:29. https://doi.org/10.3390/FERMENTATION5010029

Haile M, Kang WH (2019b) The role of microbes in coffee fermentation and their ımpact on coffee quality. J Food Qual. https://doi.org/10.1155/2019/4836709

Hamid Abadi Sherahi M, Shahidi F, Yazdi FT, Hashemi SMB (2018) Effect of Lactobacillus plantarum on olive and olive oil quality during fermentation process. LWT 89:572–580. https://doi.org/10.1016/J.LWT.2017.10.025

Han YM, Kang EA, Min Park J, Young Oh J, Yoon Lee D, Hye Choi S, Baik HK (2020) Dietary intake of fermented kimchi prevented colitis-associated cancer. J Clin Biochem Nutr 67(3):263–273. https://doi.org/10.3164/jcbn.20-77

Hancioǧlu Ö, Karapinar M (1997) Microflora of Boza, a traditional fermented Turkish beverage. Int J Food Microbiol 35(3):271–274. https://doi.org/10.1016/S0168-1605(96)01230-5

Hati S, Patel M, Mishra BK, Das S (2019) Short-chain fatty acid and vitamin production potentials of Lactobacillus isolated from fermented foods of Khasi Tribes, Meghalaya, India. Ann Microbiol 69(11):1191–1199. https://doi.org/10.1007/s13213-019-01500-8

Hikmetoglu M, Sogut E, Sogut O, Gokirmakli C, Guzel-Seydim ZB (2020) Changes in carbohydrate profile in kefir fermentation. Bioactive Carbohydr Diet Fibre 23:100220. https://doi.org/10.1016/j.bcdf.2020.100220

Hirata S, Kunisawa J (2017) Gut microbiome, metabolome, and allergic diseases. Allergol Int 66(4):523–528. https://doi.org/10.1016/j.alit.2017.06.008

Ho CC (1986) Identity and characteristics of Neurospora intermedia responsible for oncom fermentation in Indonesia. Food Microbiol 3(2):115–132. https://doi.org/10.1016/S0740-0020(86)80035-1

Ho VTT, Fleet GH, Zhao J (2018) Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms. Int J Food Microbiol 279:43–56. https://doi.org/10.1016/J.IJFOODMICRO.2018.04.040

Holck A, Axelsson L, McLeod A, Rode TM, Heir E (2017) Health and safety considerations of fermented sausages. J Food Qual. https://doi.org/10.1155/2017/9753894

Hoseinifar SH, Sharifian M, Vesaghi MJ, Khalili M, Esteban MÁ (2014) The effects of dietary xylooligosaccharide on mucosal parameters, intestinal microbiota and morphology and growth performance of Caspian white fish ( Rutilus frisii kutum) fry. Fish Shellfish Immunol 39(2):231–236. https://doi.org/10.1016/j.fsi.2014.05.009

Hotessa N, Robe J (2020) Ethiopian indigenous traditional fermented beverage: the role of the microorganisms toward nutritional and safety value of fermented beverage. Int J Microbiol. https://doi.org/10.1155/2020/8891259

Im S, Lee MK, Yun YM, Cho SK, Kim DH (2020) Effect of storage time and temperature on hydrogen fermentation of food waste. Int J Hydrogen Energy 45(6):3769–3775. https://doi.org/10.1016/j.ijhydene.2019.06.215

Iraporda C, Errea A, Romanin DE, Cayet D, Pereyra E, Pignataro O, Sirard JC, Garrote GL, Abraham AG, Rumbo M (2015) Lactate and short chain fatty acids produced by microbial fermentation downregulate proinflammatory responses in intestinal epithelial cells and myeloid cells. Immunobiology 220(10):1161–1169. https://doi.org/10.1016/j.imbio.2015.06.004

Irwin JA (2020) Overview of extremophiles and their food and medical applications. In: Salwan R, Sharma V (eds) Physiological and biotechnological aspects of extremophiles. Academic Press, pp 65–87. https://doi.org/10.1016/B978-0-12-818322-9.00006-X

Ishangulyyev R, Kim S, Lee S (2019) Understanding food loss and waste-why are we losing and wasting food? Foods 8(8):297. https://doi.org/10.3390/foods8080297

Jamal P, Akbar I (2016) Process development for maximum lycopene production from selected fruit waste and its antioxidant and antiradical activity. J Food Process Technol. https://doi.org/10.4172/2157-7110.1000576

Jamir B, Deb CR (2021) Nutritional and microbiological study of anishi: a traditional fermented food product of Nagaland, India. J Adv Food Sci Technol 4(3):113–121

Google Scholar  

Jang SH, Sim SY, Ahn HY, Seo KI, Cho YS (2018) Physicochemical properties and biological activities of Tenebrio molitor fermented by several kinds of micro-organisms. J Life Sci 28(8):923–930. https://doi.org/10.5352/JLS.2018.28.8.923

Jeong SY, Kim E, Zhang M, Lee Y-S, Ji B, Lee S-H, Cheong YE, Yun S-I, Kim Y-S, Kim KH, Kim MS, Chun HS, Kim S (2021) Antidiabetic effect of noodles containing fermented lettuce extracts. Metabolites 11(8):520. https://doi.org/10.3390/metabo11080520

Jeyaram K, Romi W, Singh TA, Devi AR, Devi SS (2010) Bacterial species associated with traditional starter cultures used for fermented bamboo shoot production in Manipur state of India. Int J Food Microbiol 143(1–2):1–8. https://doi.org/10.1016/J.IJFOODMICRO.2010.07.008

Jiang X, Ding H, Liu Q, Wei Y, Zhang Y, Wang Y, Lu Y, Ma A, Li Z, Hu Y (2020) Effects of peanut meal extracts fermented by Bacillus natto on the growth performance, learning and memory skills and gut microbiota modulation in mice. Br J Nutr 123(4):383–393. https://doi.org/10.1017/S0007114519002988

Joët T, Laffargue A, Descroix F, Doulbeau S, Bertrand B, kochko, A. de, and Dussert, S. (2010) Influence of environmental factors, wet processing and their interactions on the biochemical composition of green Arabica coffee beans. Food Chem 118(3):693–701. https://doi.org/10.1016/J.FOODCHEM.2009.05.048

Joishy TK, Dehingia M, Khan MR (2019) Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk. World J Microbiol Biotechnol 35(7):102. https://doi.org/10.1007/s11274-019-2677-y

Jones SE, Paynich ML, Kearns DB, Knight KL (2014) Protection from intestinal inflammation by bacterial exopolysaccharides. J Immunol 192(10):4813–4820. https://doi.org/10.4049/jimmunol.1303369

Joung H, Kim B, Park H, Lee K, Kim HH, Sim HC, Do HJ, Hyun CK, Do MS (2017) Fermented Moringa oleifera decreases hepatic adiposity and ameliorates glucose intolerance in high-fat diet-induced obese mice. J Med Food 20(5):439–447. https://doi.org/10.1089/jmf.2016.3860

Juárez-Castelán C, García-Cano I, Escobar-Zepeda A, Azaola-Espinosa A, Álvarez-Cisneros Y, Ponce-Alquicira E (2019) Evaluation of the bacterial diversity of Spanish-type chorizo during the ripening process using high-throughput sequencing and physicochemical characterization. Meat Sci 150:7–13. https://doi.org/10.1016/j.meatsci.2018.09.001

Kabak B, Dobson ADW (2011) An introduction to the traditional fermented foods and beverages of Turkey. Crit Rev Food Sci Nutr 51(3):248–260. https://doi.org/10.1080/10408390903569640

Kamiloğlu A (2022) Functional and technological characterization of lactic acid bacteria isolated from Turkish dry-fermented sausage (sucuk). Braz J Microbiol 53(2):959–968. https://doi.org/10.1007/s42770-022-00708-2

Kang CH, Kim JS, Park HM, Kim S, Paek NS (2021) Antioxidant activity and short-chain fatty acid production of lactic acid bacteria isolated from Korean individuals and fermented foods. 3 Biotech 11(5):217. https://doi.org/10.1007/s13205-021-02767-y

Kannengiesser J, Sakaguchi-Söder K, Mrukwia T, Jager J, Schebek L (2016) Extraction of medium chain fatty acids from organic municipal waste and subsequent production of bio-based fuels. Waste Manage 47:78–83. https://doi.org/10.1016/j.wasman.2015.05.030

Kantachote D, Ratanaburee A, Sukhoom A, Sumpradit T, Asavaroungpipop N (2015) Use of -aminobutyric acid producing lactic acid bacteria as starters to reduce biogenic amines and cholesterol in Thai fermented pork sausage (Nham) and their distribution during fermentation. LWT 70:171–177. https://doi.org/10.1016/j.lwt.2016.02.041

Kaur H, Kaur G, Ali SA (2022) Dairy-based probiotic-fermented functional foods: an update on their health-promoting properties. Fermentation 8(9):425. https://doi.org/10.3390/fermentation8090425

Kayodé AP, Hounhouigan DJ, Nout MJ, Niehof A (2007) Household production of sorghum beer in Benin: technological and socio-economic aspects. Int J Consum Stud 31(3):258–264. https://doi.org/10.1111/j.1470-6431.2006.00546.x

Kewuyemi YO, Kesa H, Chinma CE, Adebo OA (2020) Fermented edible insects for promoting food security in Africa. InSects 11(5):283. https://doi.org/10.3390/insects11050283

Khurana RK, Jain A, Jain A, Sharma T, Singh B, Kesharwani P (2018) Administration of antioxidants in cancer: debate of the decade. Drug Discov Today 23(4):763–770. https://doi.org/10.1016/j.drudis.2018.01.021

Kieliszek M, Pobiega K, Piwowarek K, Kot AM (2021) Characteristics of the proteolytic enzymes produced by lactic acid bacteria. Molecules 26(7):1858. https://doi.org/10.3390/molecules26071858

Kim HY, Park KY (2018) Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults. J Funct Foods 47:325–333. https://doi.org/10.1016/j.jff.2018.05.052

Kim JA, Bayo J, Cha J, Choi YJ, Jung MY, Kim DH, Kim Y (2019) Investigating the probiotic characteristics of four microbial strains with potential application in feed industry. PloS one 14(6):e0218922. https://doi.org/10.1371/journal.pone.0218922

Knorr D, Augustin MA (2022) Food systems at a watershed: Unlocking the benefits of technology and ecosystem symbioses. Crit Rev Food Sci Nutr. https://doi.org/10.1080/10408398.2021.2023092

Kok CR, Hutkins R (2018) Yogurt and other fermented foods as sources of health-promoting bacteria. Nutr Rev 76:4–15. https://doi.org/10.1093/nutrit/nuy056

Kondybayev A, Loiseau G, Achir N, Mestres C, Konuspayeva G (2021) Fermented mare milk product (Qymyz, Koumiss). Int Dairy J 119:105065. https://doi.org/10.1016/j.idairyj.2021.105065

Koskinen TT, Virtanen HEK, Voutilainen S, Tuomainen T-P, Mursu J, Virtanen JK (2018) Intake of fermented and non-fermented dairy products and risk of incident CHD: the Kuopio Ischaemic Heart Disease Risk Factor Study. Br J Nutr 120(11):1288–1297. https://doi.org/10.1017/S0007114518002830

Kroger M, Kurmann J, Rasic J (1992) Fermented milks—Past, present, and future. In Applications of biotechnology to traditional fermented foods. National Academy Press, p 61

Krüger A, Schäfers C, Schröder C, Antranikian G (2018) Towards a sustainable biobased industry. Highlighting the impact of extremophiles. N Biotechnol 40:144–153. https://doi.org/10.1016/j.nbt.2017.05.002

Kudumija N, Vulić A, Lešić T, Vahčić N, Pleadin J (2020) Aflatoxins and ochratoxin A in dry-fermented sausages in Croatia, by LC-MS/MS. Food Addit Contam Part B 13(4):225–232. https://doi.org/10.1080/19393210.2020.1762760

Kumar A (2017) Role of microbes in dairy industry. Nutr Food Sci Int J. https://doi.org/10.19080/nfsij.2017.03.555612

Kumar P, Chatli MK, Verma AK, Mehta N, Malav OP, Kumar D, Sharma N (2017) Quality, functionality, and shelf life of fermented meat and meat products: A review. Crit Rev Food Sci Nutr 57(13):2844–2856. https://doi.org/10.1080/10408398.2015.1074533

Kumar A, Thakur A, Panesar PS (2019) Recent developments on sustainable solvents for emulsion liquid membrane processes. J Clean Prod 240:118250. https://doi.org/10.1016/j.jclepro.2019.118250

Kwak SH, Cho YM, Noh GM, Om AS (2014) Cancer Preventive potential of kimchi lactic acid bacteria ( Weissella cibaria , Lactobacillus plantarum ). J Cancer Prev 19(4):253. https://doi.org/10.15430/JCP.2014.19.4.253

La Torre GL, Cicero N, Bartolomeo G, Rando R, Vadalà R, Santini A, Durazzo A, Lucarini M, Dugo G, Salvo A (2020) Assessment and monitoring of fish quality from a coastal ecosystem under high anthropic pressure: a case study in Southern Italy. Int J Environ Res Public Health 17(9):3285. https://doi.org/10.3390/ijerph17093285

Lahiri D, Nag M, Sarkar T, Ray RR, Shariati MA, Rebezov M, Bangar SP, Lorenzo JM, Domínguez R (2022) Lactic acid bacteria (LAB): autochthonous and probiotic microbes for meat preservation and fortification. Foods 11:2792. https://doi.org/10.3390/foods11182792

Landeta G, Curiel JA, Carrascosa AV, Muñoz R, de las Rivas B (2013) Technological and safety properties of lactic acid bacteria isolated from Spanish dry-cured sausages. Meat Sci 95(2):272–280. https://doi.org/10.1016/j.meatsci.2013.05.019

Landeta-Salgado C, Cicatiello P, Lienqueo ME (2021) Mycoprotein and hydrophobin like protein produced from marine fungi Paradendryphiella salina in submerged fermentation with green seaweed Ulva spp. Algal Res 56:102314. https://doi.org/10.1016/J.ALGAL.2021.102314

Landis EA, Oliverio AM, McKenney EA, Nichols LM, Kfoury N, Biango-Daniels M, Shell LK, Madden AA, Shapiro L, Sakunala S, Drake K, Robbat A, Booker M, Dunn RR, Fierer N, Wolfe BE (2021) The diversity and function of sourdough starter microbiomes. Elife 10:e61644. https://doi.org/10.7554/eLife.61644

Lavefve L, Marasini D, Carbonero F (2019) Microbial ecology of fermented vegetables and non-alcoholic drinks and current knowledge on their impact on human health. Adv Food Nutr Res 87:147–185. https://doi.org/10.1016/BS.AFNR.2018.09.001

Lee MH, Li FZ, Lee J, Kang J, Lim SI, Nam YD (2017) Next-generation sequencing analyses of bacterial community structures in soybean pastes produced in Northeast China. J Food Sci 82(4):960–968. https://doi.org/10.1111/1750-3841.13665

Lee CS, Lee SH, Kim SH (2020) Bone-protective effects of Lactobacillus plantarum B719-fermented milk product. Int J Dairy Technol 73(4):706–717. https://doi.org/10.1111/1471-0307.12701

Leite P, Silva C, Salgado JM, Belo I (2019) Simultaneous production of lignocellulolytic enzymes and extraction of antioxidant compounds by solid-state fermentation of agro-industrial wastes. Ind Crops Prod 137:315–322. https://doi.org/10.1016/j.indcrop.2019.04.044

Li KJ, Burton-Pimentel KJ, Vergères G, Feskens EJM, Brouwer-Brolsma EM (2022) Fermented foods and cardiometabolic health: definitions, current evidence, and future perspectives. Front Nutr 9:976020. https://doi.org/10.3389/fnut.2022.976020

Li Z, Dong Y, Zhang Y, Zheng M, Jiang Z, Zhu Y, Deng S, Li Q, Ni H (2023) Lactobacillus-fermentation enhances nutritional value and improves the inhibition on pancreatic lipase and oral pathogens of edible red seaweed Bangia fusco-purpurea . LWT. https://doi.org/10.1016/J.LWT.2023.114643

Lin W, Lin M, Zhou H, Wu H, Li Z, Lin W (2019) The effects of chemical and organic fertilizer usage on rhizosphere soil in tea orchards. PLoS ONE 14(5):e0217018. https://doi.org/10.1371/journal.pone.0217018

Linder T (2019) Making the case for edible microorganisms as an integral part of a more sustainable and resilient food production system. Food Secur 11(2):265–278. https://doi.org/10.1007/s12571-019-00912-3

Liu W, Wang J, Zhang J, Mi Z, Gesudu Q, Sun T (2019) Dynamic evaluation of the nutritional composition of homemade koumiss from Inner Mongolia during the fermentation process. J Food Process Preserv. https://doi.org/10.1111/jfpp.14022

Lopitz-Otsoa F, Rementeria A, Elguezabal N, Garaizar J (2006) Kefir: A symbiotic yeasts-bacteria community with alleged healthy capabilities. Revista Iberoamericana De Micologia 23(2):67–74. https://doi.org/10.1016/s1130-1406(06)70016-x

Lu S, Chen S, Li H, Paengkoum S, Taethaisong N, Meethip W, Surakhunthod J, Sinpru B, Sroichak T, Archa P, Thongpea S, Paengkoum P (2022) Sustainable valorization of tomato pomace ( Lycopersicon esculentum ) in animal nutrition: a review. Animals 12(23):3294. https://doi.org/10.3390/ani12233294

Luo L, Sriram S, Johnravindar D, Martin LP, T., Wong, J. W. C., and Pradhan, N. (2022) Effect of inoculum pretreatment on the microbial and metabolic dynamics of food waste dark fermentation. Biores Technol 358:127404. https://doi.org/10.1016/j.biortech.2022.127404

Luz C, Calpe J, Manuel Quiles J, Torrijos R, Vento M, Gormaz M, Mañes J, Meca G (2021) Probiotic characterization of Lactobacillus strains isolated from breast milk and employment for the elaboration of a fermented milk product. J Funct Foods 84:104599. https://doi.org/10.1016/j.jff.2021.104599

Lyu X, Lee J, Chen WN (2019) Potential natural food preservatives and their sustainable production in yeast: terpenoids and polyphenols. J Agric Food Chem 67(16):4397–4417. https://doi.org/10.1021/acs.jafc.8b07141

Lyumugabe F, Kamaliza G, Bajyana E, Thonart P (2010) Microbiological and physico-chemical characteristic of Rwandese traditional beer “Ikigage.” Afr J Biotech 9:4241–4246

Ma H, Zhao Y, Huang W, Zhang L, Wu F, Ye J, Chen GQ (2020) Rational flux-tuning of Halomonas bluephagenesis for co-production of bioplastic PHB and ectoine. Nat Commun 11(1):3313. https://doi.org/10.1038/s41467-020-17223-3

Macori G, Cotter PD (2018) Novel insights into the microbiology of fermented dairy foods. Curr Opin Biotechnol 49:172–178. https://doi.org/10.1016/j.copbio.2017.09.002

Maiorano G, Ramires FA, Durante M, Palamà IE, Blando F, De Rinaldis G, Perbellini E, Patruno V, Gadaleta Caldarola C, Vitucci S, Mita G, Bleve G (2022) The controlled semi-solid fermentation of seaweeds as a strategy for their stabilization and new food applications. Foods. https://doi.org/10.3390/FOODS11182811

Mancini S, Moruzzo R, Riccioli F, Paci G (2019) European consumers’ readiness to adopt insects as food. A Review. Food Res Int 122:661–678. https://doi.org/10.1016/j.foodres.2019.01.041

Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A, Smid EJ, Hutkins R (2017) Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol 44:94–102. https://doi.org/10.1016/J.COPBIO.2016.11.010

Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R (2021) The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 18(3):196–208. https://doi.org/10.1038/s41575-020-00390-5

Martin-Rios C, Hofmann A, Mackenzie N (2021) Sustainability-oriented innovations in food waste management technology. Sustainability 13:210. https://doi.org/10.3390/su13010210

Mathur H, Beresford TP, Cotter PD (2020) Health benefits of lactic acid bacteria (LAB) fermentates. Nutrients 12(6):1679. https://doi.org/10.3390/nu12061679

Mawonike R, Chigunyeni B, Chipumuro M (2018) Process improvement of opaque beer (chibuku) based on multivariate cumulative sum control chart. J Inst Brew 124(1):16–22. https://doi.org/10.1002/JIB.466

Melikoglu M, Lin C, Webb C (2013) Analysing global food waste problem: Pinpointing the facts and estimating the energy content. Open Engineering 3(2):157–164. https://doi.org/10.2478/s13531-012-0058-5

Mendoza-Salazar A, Santiago-López L, Torres-Llanez MJ, Hernández-Mendoza A, Vallejo-Cordoba B, Liceaga AM, González-Córdova AF (2021) In vitro antioxidant and antihypertensive activity of edible insects flours (Mealworm and Grasshopper) fermented with Lactococcus lactis Strains. Fermentation 7(3):153. https://doi.org/10.3390/fermentation7030153

Metras BN, Holle MJ, Parker VJ, Miller MJ, Swanson KS (2021) Commercial kefir products assessed for label accuracy of microbial composition and density. JDS Commun 2(3):87–91. https://doi.org/10.3168/jdsc.2020-0056

Michel F, Hartmann C, Siegrist M (2021) Consumers’ associations, perceptions and acceptance of meat and plant-based meat alternatives. Food Qual Prefer 87:104063. https://doi.org/10.1016/J.FOODQUAL.2020.104063

Milicevic B, Tomović V, Danilović B, Savić D (2021) The influence of starter cultures on the lactic acid bacteria microbiota of Petrovac sausage. Ital J Food Sci 33(2):24–34. https://doi.org/10.15586/ijfs.v33i2.1918

Miller KK, Alper HS (2019) Yarrowia lipolytica : more than an oleaginous workhorse. Appl Microbiol Biotechnol 103:9251–9262. https://doi.org/10.1007/s00253-019-10200-x

Mir SA, Raja J, Masoodi FA (2018) Fermented vegetables, a rich repository of beneficial probiotics—a review. Ferment Technol 7(1):1–6. https://doi.org/10.4172/2167-7972.1000150

Mok WK, Tan YX, Lee J, Kim J, Chen WN (2019) A metabolomic approach to understand the solid-state fermentation of okara using Bacillus subtilis WX-17 for enhanced nutritional profile. AMB Expr 9(1):60. https://doi.org/10.1186/s13568-019-0786-5

Mongkolwai T, Assavanig A, Amnajsongsiri C, Flegel TW, Bhumiratana A (1997) Technology transfer for small and medium soy sauce fermentation factories in Thailand: a consortium approach. Food Res Int 30(8):555–563. https://doi.org/10.1016/S0963-9969(98)00033-7

Monteiro P, Lomartire S, Cotas J, Pacheco D, Marques JC, Pereira L, Gonçalves AMM (2021) Seaweeds as a fermentation substrate: a challenge for the food processing industry. Processes 9(11):1953. https://doi.org/10.3390/PR9111953

Moore JF, DuVivier R, Johanningsmeier SD (2021) Formation of γ-aminobutyric acid (GABA) during the natural lactic acid fermentation of cucumber. J Food Compos Anal 96:103711. https://doi.org/10.1016/J.JFCA.2020.103711

Moradi M, Kousheh SA, Almasi H, Alizadeh A, Guimarães JT, Yılmaz N, Lotfi A (2020) Postbiotics produced by lactic acid bacteria: the next frontier in food safety. Compr Rev Food Sci Food Saf 19(6):3390–3415. https://doi.org/10.1111/1541-4337.12613

Motey GA, Owusu-Kwarteng J, Obiri-Danso K, Ofori LA, Ellis WO, Jespersen L (2021) In vitro properties of potential probiotic lactic acid bacteria originating from Ghanaian indigenous fermented milk products. World J Microbiol Biotechnol 37(3):52. https://doi.org/10.1007/s11274-021-03013-6

Mouritsen OG, Duelund L, Calleja G, Frøst MB (2017) Flavour of fermented fish, insect, game, and pea sauces: garum revisited. Int J Gastronomy Food Sci 9:16–28. https://doi.org/10.1016/j.ijgfs.2017.05.002

Mukherjee A, Gómez-Sala B, O’Connor EM, Kenny JG, Cotter PD (2022) Global regulatory frameworks for fermented foods: a review. Front Nutr 9:902642. https://doi.org/10.3389/fnut.2022.902642

Muncan J, Tei K, Tsenkova R (2020) Real-time monitoring of yogurt fermentation process by aquaphotomics near-infrared spectroscopy. Sensors 21(1):177. https://doi.org/10.3390/s21010177

Munesue Y, Masui T, Fushima T (2015) The effects of reducing food losses and food waste on global food insecurity, natural resources, and greenhouse gas emissions. Environ Econ Policy Stud 17(1):43–77. https://doi.org/10.1007/s10018-014-0083-0

Muunda E, Mtimet N, Bett E, Wanyoike F, Alonso S (2023) Milk purchase and consumption patterns in peri-urban low-income households in Kenya. Front Sustain Food Syst 7:1084067. https://doi.org/10.3389/fsufs.2023.1084067

Muyanja C, Kikafunda J, Narvhus JA, Helgetun K, Langsrud T (2003) Production methods and composition of bushera: a Ugandan traditional fermented cereal beverage. Afr J Food Agric Nutr Dev 3(1):10–19. https://doi.org/10.4314/ajfand.v3i1.19108

Milinovic J, Mata P, Diniz M, Noronha JP (2021) Umami taste in edible seaweeds: The current comprehension and perception. Int J Gastron Food Sci 23: 100301. https://doi.org/10.1016/j.ijgfs.2020.100301

Nagarajan S, Jones RJ, Oram L, Massanet-Nicolau J, Guwy A (2022) Intensification of acidogenic fermentation for the production of biohydrogen and volatile fatty acids-a perspective. Fermentation 8(7):7. https://doi.org/10.3390/fermentation8070325

Nampoothiri KM, Beena DJ, Vasanthakumari DS, Ismail B (2017) Health benefits of exopolysaccharides in fermented foods. In: Frias J, Martinez-Villaluenga C, Peñas E (eds) Fermented foods in health and disease prevention. Elsevier, pp 49–62. https://doi.org/10.1016/B978-0-12-802309-9.00003-0

Nejati F, Rizzello CG, Di Cagno R, Sheikh-Zeinoddin M, Diviccaro A, Minervini F, Gobbetti M (2013) Manufacture of a functional fermented milk enriched of Angiotensin-I Converting Enzyme (ACE)-inhibitory peptides and γ-amino butyric acid (GABA). LWT Food Sci Technol 51(1):183–189. https://doi.org/10.1016/j.lwt.2012.09.017

Nemeth A, Kaleta Z (2015) Complex utilization of dairy waste (whey) in biorefinery. WSEAS Trans Environ Dev 11:80–88

Neves Casarotti S, Fernanda Borgonovi T, de Mello Tieghi T, Sivieri K, Penna LBA (2020) Probiotic low-fat fermented goat milk with passion fruit by-product: In vitro effect on obese individuals’ microbiota and on metabolites production. Food Res Int 136:109453. https://doi.org/10.1016/j.foodres.2020.109453

Ng HS, Kee PE, Yim HS, Chen P-T, Wei Y-H, Chi-Wei Lan J (2020) Recent advances on the sustainable approaches for conversion and reutilization of food wastes to valuable bioproducts. Biores Technol 302:122889. https://doi.org/10.1016/j.biortech.2020.122889

Nishida K, Sawada D, Kawai T, Kuwano Y, Fujiwara S, Rokutan K (2017) Para-psychobiotic Lactobacillus gasseri 2305 ameliorates stress-related symptoms and sleep quality. J Appl Microbiol 123(6):1561–1570. https://doi.org/10.1111/jam.13594

Niva M, Vainio A (2021) Towards more environmentally sustainable diets? Changes in the consumption of beef and plant- and insect-based protein products in consumer groups in Finland. Meat Sci. https://doi.org/10.1016/J.MEATSCI.2021.108635

Noh BS, Seo HY, Park WS, Oh S (2016) Safety of Kimchi. In: Prakash V, Martín-Belloso O, Keener L, Astley S, Braun S, McMahon H, Lelieveld H (eds) Regulating safety of traditional and ethnic foods. Academic Press, pp 369–380. https://doi.org/10.1016/B978-0-12-800605-4.00019-0

Nongdam P (2015) Traditional fermented bamboo shoot foods of North-East India and their characteristic natural microbial flora. 10th World Bamboo Congress, Korea 2015

Nongonierma AB, FitzGerald RJ (2015) The scientific evidence for the role of milk protein-derived bioactive peptides in humans: a review. J Funct Foods 17:640–656. https://doi.org/10.1016/j.jff.2015.06.021

Norakma MN, Zaibunnisa AH, Razarinah WARW (2022) The changes of phenolics profiles, amino acids and volatile compounds of fermented seaweed extracts obtained through microbial fermentation. Mater Today Proc 48:815–821. https://doi.org/10.1016/J.MATPR.2021.02.366

Nout MJR, Kok B, Vela E, Nche PF, Rombouts FM (1995) Acceleration of the fermentation of kenkey, an indigenous fermented maize food of Ghana. Food Res Int 28(6):599–604. https://doi.org/10.1016/0963-9969(95)00059-3

Nxumalo Z, Thimiri Govinda Raj DB (2020) Application and challenges of synthetic biology. In: Singh V (ed) Advances in synthetic biology. Springer, Singapore. https://doi.org/10.1007/978-981-15-0081-7_18

O’Connor J, Hoang SA, Bradney L, Dutta S, Xiong X, Tsang DCW, Ramadass K, Vinu A, Kirkham MB, Bolan NS (2021) A review on the valorisation of food waste as a nutrient source and soil amendment. Environ Pollut 272:115985. https://doi.org/10.1016/j.envpol.2020.115985

Okoniewski A, Dobrzyńska M, Kusyk P, Dziedzic K, Przysławski J, Drzymała-Czyż S (2023) The role of fermented dairy products on gut microbiota composition. Fermentation 9:231. https://doi.org/10.3390/fermentation9030231

Ortiz-Sanchez M, Inocencio-García P-J, Alzate-Ramírez AF, Alzate CAC (2023) Potential and restrictions of food-waste valorization through fermentation processes. Fermentation 9(3):3. https://doi.org/10.3390/fermentation9030274

Østergaard DK (2019) The role of microorganisms in soy sauce production. Adv Appl Microbiol 108:45–113. https://doi.org/10.1016/bs.aambs.2019.07.002

Østergaard A, Embarek PKB, Yamprayoon J, Wedell-Neergaard C, Huss HH, Gram L (1998) Fermentation and spoilage of som fak, a Thai low-salt fish product. Trop Sci 38:105–112

Ouyang P, Wang H, Hajnal I, Wu Q, Guo Y, Chen GQ (2018) Increasing oxygen availability for improving poly(3-hydroxybutyrate) production by Halomonas. Metab Eng 45:20–31. https://doi.org/10.1016/j.ymben.2017.11.006

Öz E, Kaban G, Barış Ö, Kaya M (2017) Isolation and identification of lactic acid bacteria from pastırma. Food Control 77:158–162. https://doi.org/10.1016/j.foodcont.2017.02.017

Palacios S, Ruiz HA, Ramos-Gonzalez R, Martínez J, Segura E, Aguilar M, Aguilera A, Michelena G, Aguilar C, Ilyina A (2017) Comparison of physicochemical pretreatments of banana peels for bioethanol production. Food Sci Biotechnol 26(4):993–1001. https://doi.org/10.1007/s10068-017-0128-9

Panyawoot N, So S, Cherdthong A, Chanjula P (2022) Effect of feeding discarded durian peel ensiled with Lactobacillus casei TH14 and additives in total mixed rations on digestibility, ruminal fermentation, methane mitigation, and nitrogen balance of Thai Native–Anglo-Nubian goats. Fermentation 8(2):2. https://doi.org/10.3390/fermentation8020043

Paramithiotis S, Das G, Shin H-S, Patra JK (2022) Fate of bioactive compounds during lactic acid fermentation of fruits and vegetables. Foods 11(5):733. https://doi.org/10.3390/foods11050733

Parente E, Cogan TM, Powell IB (2017) Starter cultures: general aspects. In: McSweeney PLH, Fox PF, Cotter PD, Everett DW (eds) Dairy and dairy products. Academic Press, pp 201–226. https://doi.org/10.1016/B978-0-12-417012-4.00008-9

Park S, Bae JH (2016) Fermented food intake is associated with a reduced likelihood of atopic dermatitis in an adult population (Korean National Health and Nutrition Examination Survey 2012–2013). Nutr Res 36(2):125–133. https://doi.org/10.1016/j.nutres.2015.11.011

Parlindungan E, Lugli GA, Ventura M, van Sinderen D, Mahony J (2021) Lactic acid bacteria diversity and characterization of probiotic candidates in fermented meats. Foods 10(7):1519. https://doi.org/10.3390/foods10071519

Patel A, Prajapat J (2013) Food and health applications of exopolysaccharides produced by lactic acid bacteria. Adv Dairy Res. https://doi.org/10.4172/2329-888x.1000107

Pérez-Alva A, MacIntosh AJ, Baigts-Allende DK, García-Torres R, Ramírez-Rodrigues MM (2022) Fermentation of algae to enhance their bioactive activity: a review. Algal Res 64:102684. https://doi.org/10.1016/J.ALGAL.2022.102684

Pérez-Díaz IM, Hayes J, Medina E, Anekella K, Daughtry K, Dieck S, Levi M, Price R, Butz N, Lu Z, Azcarate-Peril MA (2017) Reassessment of the succession of lactic acid bacteria in commercial cucumber fermentations and physiological and genomic features associated with their dominance. Food Microbiol 63:217–227. https://doi.org/10.1016/J.FM.2016.11.025

Pham PV (2018) Medical biotechnology: techniques and applications. In: Barh D, Azevedo V (eds) Omics technologies and bio-engineering. Academic Press, pp 449–469. https://doi.org/10.1016/B978-0-12-804659-3.00019-1

Pi X, Wan Y, Yang Y, Li R, Wu X, Xie M, Li X, Fu G (2019) Research progress in peanut allergens and their allergenicity reduction. Trends Food Sci Technol 93:212–220. https://doi.org/10.1016/j.tifs.2019.09.014

Pi X, Peng Z, Liu J, Jiang Y, Wang J, Fu G, Yang Y, Sun Y (2022) Sesame allergy: mechanisms, prevalence, allergens, residue detection, effects of processing and cross-reactivity. Crit Rev Food Sci Nutr 1–16. https://doi.org/10.1080/10408398.2022.2128031

Pihlanto A, Korhonen H (2015) Bioactive peptides from fermented foods and health promotion. In: Korhonen H (ed) Advances in fermented foods and beverages. Elsevier, pp 39–74. https://doi.org/10.1016/B978-1-78242-015-6.00003-7

Piqué N, Berlanga M, Miñana-Galbis D (2019) Health benefits of heat-killed (Tyndallized) probiotics: an overview. Int J Mol Sci 20(10):2534. https://doi.org/10.3390/ijms20102534

Pires AF, Marnotes NG, Rubio OD, Garcia AC, Pereira CD (2021) Dairy by-products: a review on the valorization of whey and second cheese whey. Foods 10(5):5. https://doi.org/10.3390/foods10051067

Pleadin J, Kovačević D, Perković I (2015) Impact of casing damaging on aflatoxin B 1 concentration during the ripening of dry-fermented meat sausages. J Immunoassay Immunochem 36(6):655–666. https://doi.org/10.1080/15321819.2015.1032306

Pleadin J, Zadravec M, Brnić D, Perković I, Škrivanko M, Kovačević D (2016) Moulds and mycotoxins detected in the regional speciality fermented sausage ‘slavonski kulen’ during a 1-year production period. Food Addit Contam Part A. https://doi.org/10.1080/19440049.2016.1266395

Pleadin J, Lešić T, Milićević D, Markov K, Šarkanj B, Vahčić N, Kmetič I, Zadravec M (2021) Pathways of mycotoxin occurrence in meat products: a review. Processes 9(12):2122. https://doi.org/10.3390/pr9122122

Połka J, Rebecchi A, Pisacane V, Morelli L, Puglisi E (2015) Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons. Food Microbiol 46:342–356. https://doi.org/10.1016/j.fm.2014.08.023

Prado N, Sampayo M, González P, Lombó F, Díaz J (2019) Physicochemical, sensory and microbiological characterization of Asturian Chorizo, a traditional fermented sausage manufactured in Northern Spain. Meat Sci 156:118–124. https://doi.org/10.1016/j.meatsci.2019.05.023

Profeta A, Baune MC, Smetana S, Bornkessel S, Broucke K, van Royen G, Enneking U, Weiss J, Heinz V, Hieke S, Terjung N (2021) Preferences of German consumers for meat products blended with plant-based proteins. Sustainability 13(2):650. https://doi.org/10.3390/SU13020650

Rabie MA, Peres C, Malcata FX (2014) Evolution of amino acids and biogenic amines throughout storage in sausages made of horse, beef and turkey meats. Meat Sci 96(1):82–87. https://doi.org/10.1016/j.meatsci.2013.05.042

Raffaelli F, Nanetti L, Montecchiani G, Borroni F, Salvolini E, Faloia E, Ferretti G, Mazzanti L, Vignini A (2015) In vitro effects of fermented papaya ( Carica papaya L.) on platelets obtained from patients with type 2 diabetes. Nutr Metab Cardiovasc Dis 25(2):224–229. https://doi.org/10.1016/j.numecd.2014.10.013

Ranadheera CS, Evans CA, Adams MC, Baines SK (2012) In vitro analysis of gastrointestinal tolerance and intestinal cell adhesion of probiotics in goat’s milk ice cream and yogurt. Food Res Int 49(2):619–625. https://doi.org/10.1016/j.foodres.2012.09.007

Rastogi YR, Thakur R, Thakur P, Mittal A, Chakrabarti S, Siwal SS, Thakur VK, Saini RV, Saini AK (2022) Food fermentation-significance to public health and sustainability challenges of modern diet and food systems. Int J Food Microbiol 371:109666. https://doi.org/10.1016/j.ijfoodmicro.2022.109666

Ravindran R, Jaiswal AK (2016) Exploitation of food industry waste for high-value products. Trends Biotechnol 34(1):58–69. https://doi.org/10.1016/j.tibtech.2015.10.008

Ravyts F, Vuyst LD, Leroy F (2012) Bacterial diversity and functionalities in food fermentations. Eng Life Sci 12(4):356–367. https://doi.org/10.1002/elsc.201100119

Read QD, Brown S, Cuéllar AD, Finn SM, Gephart JA, Marston LT, Meyer E, Weitz KA, Muth MK (2020) Assessing the environmental impacts of halving food loss and waste along the food supply chain. Sci Total Environ 712:136255. https://doi.org/10.1016/j.scitotenv.2019.136255

RedCorn R, Engelberth AS (2016) Identifying conditions to optimize lactic acid production from food waste co-digested with primary sludge. Biochem Eng J 105:205–213. https://doi.org/10.1016/j.bej.2015.09.014

Ricci G, Andreozzi L, Cipriani F, Giannetti A, Gallucci M, Caffarelli C (2019) Wheat allergy in children: a comprehensive update. Medicina 55(7):400. https://doi.org/10.3390/medicina55070400

Ritala A, Häkkinen ST, Toivari M, Wiebe MG (2017) Single cell protein-state-of-the-art, industrial landscape and patents 2001–2016. Front Microbiol 8:2009. https://doi.org/10.3389/fmicb.2017.02009

Rodríguez A, Bernáldez V, Rodríguez M, Andrade MJ, Núñez F, Córdoba JJ (2015) Effect of selected protective cultures on ochratoxin A accumulation in dry-cured Iberian ham during its ripening process. LWT Food Sci Technol 60(2):923–928. https://doi.org/10.1016/j.lwt.2014.09.059

Rodríguez-Figueroa JC, González-Córdova AF, Astiazaran-García H, Vallejo-Cordoba B (2013) Hypotensive and heart rate-lowering effects in rats receiving milk fermented by specific Lactococcus lactis strains. Br J Nutr 109(5):827–833. https://doi.org/10.1017/S0007114512002115

Rosa DD, Dias MMS, Grześkowiak ŁM, Reis SA, Conceição LL, Peluzio do MCG (2017) Milk kefir: nutritional, microbiological and health benefits. Nutr Res Rev 30(1):82–96. https://doi.org/10.1017/S0954422416000275

Saad N, Delattre C, Urdaci M, Schmitter JM, Bressollier P (2013) An overview of the last advances in probiotic and prebiotic field. LWT Food Sci Technol 50(1):1–16. https://doi.org/10.1016/j.lwt.2012.05.014

Sabater C, Ruiz L, Delgado S, Ruas-Madiedo P, Margolles A (2020) Valorization of vegetable food waste and by-products through fermentation processes. Front Microbiol 11:581997. https://doi.org/10.3389/fmicb.2020.581997

Sadh P, Kumar S, Chawla P, Duhan J (2018) Fermentation: a boon for production of bioactive compounds by processing of food industries wastes (by-products). Molecules 23(10):2560. https://doi.org/10.3390/molecules23102560

Sahay S (2019) Wine enzymes: potential and practices. In: Kuddus M (ed) Enzymes in food biotechnology: production, applications, and future prospects. Academic Press, pp 73–92. https://doi.org/10.1016/B978-0-12-813280-7.00006-2

Salque M, Bogucki PI, Pyzel J, Sobkowiak-Tabaka I, Grygiel R, Szmyt M, Evershed RP (2013) Earliest evidence for cheese making in the sixth millennium bc in northern Europe. Nature 493(7433):522–525. https://doi.org/10.1038/nature11698

Şanlier N, Gökcen BB, Sezgin AC (2019) Health benefits of fermented foods. Crit Rev Food Sci Nutr 59(3):506–527. https://doi.org/10.1080/10408398.2017.1383355

Santiago-Díaz P, Rico M, Rivero A, Santana-Casiano M (2022) Bioactive metabolites of microalgae from canary ıslands for functional food and feed uses. Chem Biodivers. https://doi.org/10.1002/cbdv.202200230

Santos MHS (1996) Biogenic amines: their importance in foods. Int J Food Microbiol 29(2–3):213–231. https://doi.org/10.1016/0168-1605(95)00032-1

Saqib S, Akram A, Halim SA, Tassaduq R (2017) Sources of β-galactosidase and its applications in food industry. 3 Biotech 7(1):79. https://doi.org/10.1007/s13205-017-0645-5

Savaiano DA (2014) Lactose digestion from yogurt: mechanism and relevance. Am J Clin Nutr 99(5):1251S-1255S. https://doi.org/10.3945/ajcn.113.073023

Sawadogo-Lingani H, Owusu-Kwarteng J, Glover R, Diawara B, Jakobsen M, Jespersen L (2021) Sustainable production of african traditional beers with focus on dolo, a west african sorghum-based alcoholic beverage. Front Sustain Food Syst 5:143. https://doi.org/10.3389/FSUFS.2021.672410/BIBTEX

Schiano AN, Harwood WS, Gerard PD, Drake MA (2020) Consumer perception of the sustainability of dairy products and plant-based dairy alternatives. J Dairy Sci 103(12):11228–11243. https://doi.org/10.3168/jds.2020-18406

Sekwati-Monang B, Gänzle MG (2011) Microbiological and chemical characterisation of ting, a sorghum-based sourdough product from Botswana. Int J Food Microbiol 150(2–3):115–121. https://doi.org/10.1016/j.ijfoodmicro.2011.07.021

Seong G, Lee S, Min YW, Jang YS, Kim HS, Kim E-J, Park S-Y, Kim C-H, Chang DK (2021) Effect of heat-killed Lactobacillus casei DKGF7 on a rat model of irritable bowel syndrome. Nutrients 13(2):568. https://doi.org/10.3390/nu13020568

Sepúlveda L, Laredo-Alcalá E, Buenrostro-Figueroa JJ, Ascacio-Valdés JA, Genisheva Z, Aguilar C, Teixeira J (2020) Ellagic acid production using polyphenols from orange peel waste by submerged fermentation. Electron J Biotechnol 43:1–7. https://doi.org/10.1016/j.ejbt.2019.11.002

Shafi A, Naeem Raja H, Farooq U, Akram K, Hayat Z, Naz A, Nadeem HR (2019) Antimicrobial and antidiabetic potential of synbiotic fermented milk: a functional dairy product. Int J Dairy Technol 72(1):15–22. https://doi.org/10.1111/1471-0307.12555

Sharma I, Yaiphathoi S (2020) Role of microbial communities in traditionally fermented foods and beverages in North East India. In: Mandal SD, Bhatt P (eds) Recent advancements in microbial diversity. Academic Press, pp 445–470. https://doi.org/10.1016/B978-0-12-821265-3.00019-0

Sharma R, Garg P, Kumar P, Bhatia SK, Kulshrestha S (2020) Microbial fermentation and its role in quality improvement of fermented foods. Fermentation 6(4):106. https://doi.org/10.3390/fermentation6040106

Sivamaruthi B, Kesika P, Prasanth M, Chaiyasut C (2018) A mini review on antidiabetic properties of fermented foods. Nutrients 10(12):1973. https://doi.org/10.3390/nu10121973

Smid EJ, Kleerebezem M (2014) Production of aroma compounds in lactic fermentations. Annu Rev Food Sci Technol 5(1):313–326. https://doi.org/10.1146/annurev-food-030713-092339

Subrota H, Shilpa, Brij S, Vandna K, Surajit M (2013) Antioxidative activity and polyphenol content in fermented soy milk supplemented with WPC-70 by probiotic Lactobacilli. Int Food Res J 20(5):2125–2131

Suez J, Zmora N, Segal E, Elinav E (2019) The pros, cons, and many unknowns of probiotics. Nat Med 25(5):716–729. https://doi.org/10.1038/s41591-019-0439-x

Sun X, Zhou K, Gong Y, Zhang N, Yang M, Qing D, Li Y, Lu J, Li J, Feng C, Li C, Yang Y (2016) Determination of biogenic amines in sichuan-style spontaneously fermented sausages. Food Anal Methods 9(8):2299–2307. https://doi.org/10.1007/s12161-016-0417-6

Sun W, Shahrajabian MH, Lin M (2022) Research progress of fermented functional foods and protein factory-microbial fermentation technology. Fermentation 8(12):12. https://doi.org/10.3390/fermentation8120688

Tamang JP, Thapa N (2022) Beneficial microbiota in ethnic fermented foods and beverages. In: de Bruijn FJ, Smidt H, Cocolin LS, Sauer M, Dowling D, Thomashow L (eds) Good microbes in medicine, food production, biotechnology, bioremediation, and agriculture. Wiley, pp 130–148

Tamang JP, Tamang B, Schillinger U, Franz CMAP, Gores M, Holzapfel WH (2005) Identification of predominant lactic acid bacteria isolated from traditionally fermented vegetable products of the Eastern Himalayas. Int J Food Microbiol 105(3):347–356. https://doi.org/10.1016/J.IJFOODMICRO.2005.04.024

Tamang JP, Shin DH, Jung SJ, Chae SW (2016) Functional properties of microorganisms in fermented foods. Front Microbiol. https://doi.org/10.3389/fmicb.2016.00578

Tamang JP, Cotter PD, Endo A, Han NS, Kort R, Liu SQ, Mayo B, Westerik N, Hutkins R (2020) Fermented foods in a global age: east meets West. Compr Rev Food Sci Food Saf 19(1):184–217. https://doi.org/10.1111/1541-4337.12520

Tandon N, Gupta Y, Kapoor D, Lakshmi JK, Praveen D, Bhattacharya A, Billot L, Naheed A, De Silva A, Gupta I, Farzana N, John R, Ajanthan S, Divakar H, Bhatla N, Desai A, Pathmeswaran A, Prabhakaran D, Joshi R et al (2022) Effects of a lifestyle intervention to prevent deterioration in glycemic status among south asian women with recent gestational diabetes: a randomized clinical trial. JAMA Netw Open. https://doi.org/10.1001/jamanetworkopen.2022.0773

Tang J, Wang XC, Hu Y, Ngo HH, Li Y (2017) Dynamic membrane-assisted fermentation of food wastes for enhancing lactic acid production. Biores Technol 234:40–47. https://doi.org/10.1016/j.biortech.2017.03.019

Tasdemir SS, Sanlier N (2020) An insight into the anticancer effects of fermented foods: a review. J Funct Foods 75:104281. https://doi.org/10.1016/j.jff.2020.104281

Teng TS, Chin YL, Chai KF, Chen WN (2021) Fermentation for future food systems. EMBO Rep. https://doi.org/10.15252/embr.202152680

Terpou A, Bekatorou A, Kanellaki M, Koutinas AA, Nigam P (2017) Enhanced probiotic viability and aromatic profile of yogurts produced using wheat bran ( Triticum aestivum ) as cell immobilization carrier. Process Biochem 55:1–10. https://doi.org/10.1016/j.procbio.2017.01.013

Thakkar PN, Patel A, Modi HA, Prajapati JB (2020) Hypocholesterolemic effect of potential probiotic Lactobacillus fermentum strains isolated from traditional fermented foods in wistar rats. Probiot Antimicrob Proteins 12(3):1002–1011. https://doi.org/10.1007/s12602-019-09622-w

Thi NBD, Lin CY, Kumar G (2016) Waste-to-wealth for valorization of food waste to hydrogen and methane towards creating a sustainable ideal source of bioenergy. J Clean Prod 122:29–41. https://doi.org/10.1016/j.jclepro.2016.02.034

Thierry A, Valence F, Deutsch S-M, Even S, Falentin H, Le Loir Y, Jan G, Gagnaire V (2015) Strain-to-strain differences within lactic and propionic acid bacteria species strongly impact the properties of cheese–a review. Dairy Sci Technol 95(6):895–918. https://doi.org/10.1007/s13594-015-0267-9

Topolska K, Florkiewicz A, Filipiak-Florkiewicz A (2021) Functional food-consumer motivations and expectations. Int J Environ Res Public Health 18(10):5327. https://doi.org/10.3390/ijerph18105327

Torres-León C, Chávez-González ML, Hernández-Almanza A, Martínez-Medina GA, Ramírez-Guzmán N, Londoño-Hernández L, Aguilar CN (2021) Recent advances on the microbiological and enzymatic processing for conversion of food wastes to valuable bioproducts. Curr Opin Food Sci 38:40–45. https://doi.org/10.1016/j.cofs.2020.11.002

Tropea A (2022) Food waste valorization. Fermentation 8:168. https://doi.org/10.3390/fermentation8040168

Tropea A, Potortì AG, Lo Turco V, Russo E, Vadalà R, Rando R, Di Bella G (2021) Aquafeed production from fermented fish waste and lemon peel. Fermentation 7(4):272. https://doi.org/10.3390/fermentation7040272

Tsafack PB, Tsopmo A (2022) Effects of bioactive molecules on the concentration of biogenic amines in foods and biological systems. Heliyon 8(9):e10456. https://doi.org/10.1016/j.heliyon.2022.e10456

Tsafrakidou P, Michaelidou AM, Biliaderis CG (2020) Fermented cereal-based products: nutritional aspects, possible impact on gut microbiota and health implications. Foods. https://doi.org/10.3390/FOODS9060734

Vakhrusheva DS, Sviridenko GM, Mordvinova VA, Delitskaya IN (2022) New solutions in the technology of low-fat cheeses. IOP Conf Ser Earth Environ Sci 1052(1):012065. https://doi.org/10.1088/1755-1315/1052/1/012065

Valenti F, Porto SMC, Selvaggi R, Pecorino B (2020) Co-digestion of by-products and agricultural residues: a bioeconomy perspective for a Mediterranean feedstock mixture. Sci Total Environ 700:134440. https://doi.org/10.1016/j.scitotenv.2019.134440

Valyasevi R, Rolle RS (2002) An overview of small-scale food fermentation technologies in developing countries with special reference to Thailand: scope for their improvement. Int J Food Microbiol 75(3):231–239. https://doi.org/10.1016/S0168-1605(01)00711-5

Van Bloemendaal L, Ijzerman RG, ten Kulve JS, Barkhof F, Konrad RJ, Drent ML, Veltman DJ, Diamant M (2014) GLP-1 receptor activation modulates appetite- and reward-related brain areas in humans. Diabetes 63(12):4186–4196. https://doi.org/10.2337/db14-0849

Vasilev D, Aleksic B, Tarbuk A, Dimitrijevic M, Karabasil N, Cobanovic N, Vasiljevic N (2015) Identification of lactic acid bacteria isolated from serbian traditional fermented sausages Sremski and Lemeski Kulen. Procedia Food Sci 5:300–303. https://doi.org/10.1016/j.profoo.2015.09.071

Vasquez ZS, de Carvalho Neto DP, Pereira GVM, Vandenberghe LPS, de Oliveira PZ, Tiburcio PB, Rogez HLG, Góes Neto A, Soccol CR (2019) Biotechnological approaches for cocoa waste management: a review. Waste manag 90:72–83. https://doi.org/10.1016/j.wasman.2019.04.030

Vera-Pingitore E, Jimenez ME, Dallagnol A, Belfiore C, Fontana C, Fontana P, von Wright A, Vignolo G, Plumed-Ferrer C (2016) Screening and characterization of potential probiotic and starter bacteria for plant fermentations. LWT-Food Sci Technol 71:288–294. https://doi.org/10.1016/j.lwt.2016.03.046

Verotta L, Panzella L, Antenucci S, Calvenzani V, Tomay F, Petroni K, Caneva E, Napolitano A (2018) Fermented pomegranate wastes as sustainable source of ellagic acid: antioxidant properties, anti-inflammatory action, and controlled release under simulated digestion conditions. Food Chem 246:129–136. https://doi.org/10.1016/j.foodchem.2017.10.131

Vidhyalakshmi R, Vallinachiyar C, Radhika R (2012) Production of Xanthan from agro-industrial waste. J Adv Sci Res 3(2):56–59

Vieira Gomes A, Souza Carmo T, Silva Carvalho L, Mendonça Bahia F, Parachin N (2018) Comparison of yeasts as hosts for recombinant protein production. Microorganisms 6(2):38. https://doi.org/10.3390/microorganisms6020038

Vilela A, Bacelar E, Pinto T, Anjos R, Correia E, Gonçalves B, Cosme F (2019) Beverage and food fragrance biotechnology, novel applications, sensory and sensor techniques: an overview. Foods 8(12):12. https://doi.org/10.3390/foods8120643

Vitali B, Minervini G, Rizzello CG, Spisni E, Maccaferri S, Brigidi P, Gobbetti M, Di Cagno R (2012) Novel probiotic candidates for humans isolated from raw fruits and vegetables. Food Microbiol 31(1):116–125. https://doi.org/10.1016/J.FM.2011.12.027

Voidarou C, Antoniadou Μ, Rozos G, Tzora A, Skoufos I, Varzakas T, Lagiou A, Bezirtzoglou E (2021) Fermentative foods: microbiology, biochemistry, potential human health benefits and public health issues. Foods 10:69. https://doi.org/10.3390/foods10010069

Walhe RA, Diwanay SS, Patole MS, Sayyed RZ, Al-Shwaiman HA, Alkhulaifi MM, Elgorban AM, Danish S, Datta R (2021) Cholesterol reduction and vitamin B12 production study on Enterococcus faecium and Lactobacillus pentosus ısolated from yoghurt. Sustainability 13(11):5853. https://doi.org/10.3390/su13115853

Wanangkarn A, Liu DC, Swetwiwathana A, Jindaprasert A, Phraephaisarn C, Chumnqoen W, Tan FJ (2014) Lactic acid bacterial population dynamics during fermentation and storage of Thai fermented sausage according to restriction fragment length polymorphism analysis. Int J Food Microbiol 186:61–67. https://doi.org/10.1016/j.ijfoodmicro.2014.06.015

Wang Y, Ling C, Chen Y, Jiang X, Chen GQ (2019) Microbial engineering for easy downstream processing. Biotechnol Adv 37(6):107365. https://doi.org/10.1016/j.biotechadv.2019.03.004

Wang D, Cheng F, Wang Y, Han J, Gao F, Tian J, Zhang K, Jin Y (2022) The changes occurring in proteins during processing and storage of fermented meat products and their regulation by lactic acid bacteria. Foods 11:2427. https://doi.org/10.3390/foods11162427

Warda AK, Rea K, Fitzgerald P, Hueston C, Gonzalez-Tortuero E, Dinan TG, Hill C (2019) Heat-killed lactobacilli alter both microbiota composition and behaviour. Behav Brain Res 362:213–223. https://doi.org/10.1016/j.bbr.2018.12.047

Wedajo Lemi B (2020) Microbiology of Ethiopian traditionally fermented beverages and condiments. Int J Microbiol. https://doi.org/10.1155/2020/1478536

Wendin K, Undeland I (2020) Seaweed as food-Attitudes and preferences among Swedish consumers. A pilot study. Int J Gastronomy Food Sci 22:100265. https://doi.org/10.1016/J.IJGFS.2020.100265

Wesolowska A, Sinkiewicz-Darol E, Barbarska O, Strom K, Rutkowska M, Karzel K, Rosiak E, Oledzka G, Orczyk-Pawilowicz M, Rzoska S, Borszewska-Kornacka MK (2018) New achievements in high-pressure processing to preserve human milk bioactivity. Front Pediatr 6:323. https://doi.org/10.3389/FPED.2018.00323/BIBTEX

Xiong T, Guan Q, Song S, Hao M, Xie M (2012) Dynamic changes of lactic acid bacteria flora during Chinese sauerkraut fermentation. Food Control 26(1):178–181. https://doi.org/10.1016/J.FOODCONT.2012.01.027

Xu Y, Hlaing MM, Glagovskaia O, Augustin MA, Terefe NS (2020) Fermentation by probiotic Lactobacillus gasseri strains enhances the carotenoid and fibre contents of carrot juice. Foods 9(12):1803. https://doi.org/10.3390/foods9121803

Yalemtesfa B, Tenkegna T (2010) Solid substrate fermentation and conversion of orange waste in to fungal biomass using Aspergillus niger KA-06 and Chaetomium spp KC-06. Afr J Microbiol Res 4:1275–1281

Yan PM, Xue WT, Tan SS, Zhang H, Chang XH (2008) Effect of inoculating lactic acid bacteria starter cultures on the nitrite concentration of fermenting Chinese paocai. Food Control 19(1):50–55. https://doi.org/10.1016/J.FOODCONT.2007.02.008

Yang Y, Deng Y, Jin Y, Liu Y, Xia B, Sun Q (2017) Dynamics of microbial community during the extremely long-term fermentation process of a traditional soy sauce. J Sci Food Agric 97(10):3220–3227. https://doi.org/10.1002/JSFA.8169

Yang H, Qu Y, Li J, Liu X, Wu R, Wu J (2020) Improvement of the protein quality and degradation of allergens in soybean meal by combination fermentation and enzymatic hydrolysis. LWT 128:109442. https://doi.org/10.1016/j.lwt.2020.109442

Yang R, Chen Z, Hu P, Zhang S, Luo G (2022) Two-stage fermentation enhanced single-cell protein production by Yarrowia lipolytica from food waste. Biores Technol 361:127677. https://doi.org/10.1016/j.biortech.2022.127677

Yoon HS, Ju JH, Kim HN, Park HJ, Ji Y, Lee JE, Shin HK, Do MS, Holzapfel W (2013) Reduction in cholesterol absorption in Caco-2 cells through the down-regulation of Niemann-Pick C1-like 1 by the putative probiotic strains Lactobacillus rhamnosus BFE5264 and Lactobacillus plantarum NR74 from fermented foods. Int J Food Sci Nutr 64(1):44–52. https://doi.org/10.3109/09637486.2012.706598

Yue H, Ling C, Yang T, Chen X, Chen Y, Deng H, Wu Q, Chen J, Chen GQ (2014) A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates. Biotechnol Biofuels 7(1):108. https://doi.org/10.1186/1754-6834-7-108

Zagorec M, Champomier-Vergès MC (2023) Meat microbiology and spoilage. In: Toldrá F (ed) Woodhead publishing series in food science, technology and nutrition, Lawrie’s Meat Science, 9th edn. Elsevier, Woodhead Publishing, pp 195–218. https://doi.org/10.1016/B978-0-323-85408-5.00011-X

Zakharchenko A, Guz N, Laradji AM, Katz E, Minko S (2018) Magnetic field remotely controlled selective biocatalysis. Nat Catal 1(1):1. https://doi.org/10.1038/s41929-017-0003-3

Zeng XQ, Pan DD, Guo YX (2010) The probiotic properties of Lactobacillus buchneri P2. J Appl Microbiol 108(6):2059–2066. https://doi.org/10.1111/J.1365-2672.2009.04608.X

Zeuthen P (2007) A historical perspective of meat fermentation. In: Toldra F (ed) Handbook of fermented meat and poultry. Blackwell Publishing, Ames, Iowa, USA, p 308

Zhang Y, Li X, Bartlett DH, Xiao X (2015) Current developments in marine microbiology: high-pressure biotechnology and the genetic engineering of piezophiles. Curr Opin Biotechnol 33:157–164. https://doi.org/10.1016/j.copbio.2015.02.013

Zhang QA, Shen Y, Fan XH, García Martín JF (2016) Preliminary study of the effect of ultrasound on physicochemical properties of red wine. CyTA J Food 14(1):55–64. https://doi.org/10.1080/19476337.2015.1045036

Zhang K, Chen X, Zhang L, Deng Z (2020a) Fermented dairy foods intake and risk of cardiovascular diseases: a meta-analysis of cohort studies. Crit Rev Food Sci Nutr 60(7):1189–1194. https://doi.org/10.1080/10408398.2018.1564019

Zhang M, Dang N, Ren D, Zhao F, Lv R, Ma T, Bao Q, Menghe B, Liu W (2020b) Comparison of bacterial microbiota in raw mare’s milk and koumiss using pacbio single molecule real-time sequencing technology. Front Microbiol. https://doi.org/10.3389/fmicb.2020.581610

Zhang J, Zhao J, Li J, Xia Y, Cao J (2021) Outer membrane vesicles derived from hypervirulent Klebsiella pneumoniae stimulate the inflammatory response. Microb Pathog 154:104841. https://doi.org/10.1016/j.micpath.2021.104841

Zhang L, Liao W, Huang Y, Wen Y, Chu Y, Zhao C (2022) Global seaweed farming and processing in the past 20 years. Food Prod Process Nutr 4:23. https://doi.org/10.1186/s43014-022-00103-2

Zhao CJ, Schieber A, Gänzle MG (2016) Formation of taste-active amino acids, amino acid derivatives and peptides in food fermentations–a review. Food Res Int 89:39–47. https://doi.org/10.1016/j.foodres.2016.08.042

Zhao Y, Kumar M, Caspers MPM, Nierop Groot MN, van der Vossen JMBM, Abee T (2018) Short communication: growth of dairy isolates of Geobacillus thermoglucosidans in skim milk depends on lactose degradation products supplied by Anoxybacillus flavithermus as secondary species. J Dairy Sci 101(2):1013–1019. https://doi.org/10.3168/jds.2017-13372

Zhong H, Abdullah, Zhao M, Tang J, Deng L, Feng F (2021) Probiotics-fermented blueberry juices as potential antidiabetic product: antioxidant, antimicrobial and antidiabetic potentials. J Sci Food Agric 101(10):4420–4427. https://doi.org/10.1002/jsfa.11083

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Financial support from Nobelium Joining Gdańsk Tech Research Community (contract number DEC 33/2022/IDUB/l.1; NOBELIUM nr 036236) is gratefully acknowledged. R. Castro-Muñoz also acknowledges the School of Engineering and Science and the FEMSA-Biotechnology Center at Tecnológico de Monterrey for their support through the Bioprocess (0020209I13) Focus Group.

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Shahida Anusha Siddiqui

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Zeki Erol, Jerina Rugji, Fulya Taşçı & Hatice Ahu Kahraman

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Siddiqui, S.A., Erol, Z., Rugji, J. et al. An overview of fermentation in the food industry - looking back from a new perspective. Bioresour. Bioprocess. 10 , 85 (2023). https://doi.org/10.1186/s40643-023-00702-y

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Microbial fermentation and its role in quality improvement of fermented foods.

1. Introduction

2. enhancement of nutritional quality in fermented foods by microorganisms, 3. effects of lactic acid fermentation on the nutritional aspects of food, 4. enrichment and changes of biological components in fermented foods, 4.1. vitamins bio-enrichment, 4.2. antioxidant activity, 4.3. peptides production, 4.4. enzymes production through microorganisms, 4.5. increase in saponin and isoflavone values and poly-glutamic acid production, 4.6. anti-nutritive compounds degradation, 4.7. biochemical changes during cereal fermentation, 4.8. presence of biogenic amines in juices and vegetables fermented with lactic acid bacteria, 5. nutritional value of fermented dairy products, 6. biochemical changes in meat-based fermented food products, 7. conclusions, author contributions, acknowledgments, conflicts of interest.

• Nkhata, S.G.; Ayua, E.; Kamau, E.H.; Shingiro, J.B. Fermentation and germination improve nutritional value of cereals and legumes through activation of endogenous enzymes. Food Sci. Nutr. 2018 , 6 , 2446–2458. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Xiang, H.; Sun-Waterhouse, D.; Waterhouse, G.I.; Cui, C.; Ruan, Z. Fermentation-enabled wellness foods: A fresh perspective. Food Sci. Hum. Well. 2019 , 8 , 203–243. [ Google Scholar ] [ CrossRef ]
• Melini, F.; Melini, V.; Luziatelli, F.; Ficca, A.G.; Ruzzi, M. Health-promoting components in fermented foods: An up-to-date systematic review. Nutrients 2019 , 11 , 1189. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Sanlier, N.; Gokcen, B.B.; Sezgin, A.C. Health benefits of fermented foods. Crit. Rev. Food Sci. Nutr. 2019 , 59 , 506–527. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Okafor, N. Fermented foods and their processing. In Biotechnology-Volume VIII: Fundamentals in Biotechnology ; Eolss Publishers: Oxford, UK, 2009; Volume 8, p. 19. [ Google Scholar ]
• Mokoena, M.P. Lactic acid bacteria and their bacteriocins: Classification, biosynthesis, and applications against uropathogens: A mini-review. Molecules 2017 , 22 , 1255. [ Google Scholar ] [ CrossRef ]
• Anukam, K.C.; Reid, G. African traditional fermented foods and probiotics. J. Med. Food 2009 , 12 , 1177–1184. [ Google Scholar ] [ CrossRef ]
• Blandino, A.; Al-Aseeri, M.E.; Pandiella, S.S.; Cantero, D.; Webb, C. Cereal-based fermented foods and beverages. Food Res. Int. 2003 , 36 , 527–543. [ Google Scholar ] [ CrossRef ]
• Vagelas, I.; Gougoulias, N.; Nedesca, E.D.; Liviu, G. Bread contamination with fungus. Carpath. J. Food Sci. Technol. 2011 , 3 , 1–6. [ Google Scholar ]
• Doyle, M.P.; Meng, J. Bacteria in food and beverage production. In Prokaryotes ; Springer: New York, NY, USA, 2006; pp. 797–811. [ Google Scholar ] [ CrossRef ]
• Pessione, E. Lactic acid bacteria contribution to gut microbiota complexity: Lights and shadows. Front. Cell. Infect. Microbiol. 2012 , 2 , 86. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Pfeiffer, T.; Morley, A. An evolutionary perspective on the Crabtree effect. Front. Mol. Biosci. 2014 , 1 , 17. [ Google Scholar ] [ CrossRef ]
• Hasan, M.N.; Sultan, M.Z.; Mar-E-Um, M. Significance of fermented food in nutrition and food science. J. Sci. Res. 2014 , 6 , 373–386. [ Google Scholar ] [ CrossRef ]
• Kennedy, D.O. B vitamins and the brain: Mechanisms, dose, and efficacy—A review. Nutrients 2016 , 8 , 68. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Potter, N.N.; Hotchkiss, J.H. Food Science , 5th ed.; C.B.S. Publishers and Distributors: New Delhi, India, 2006; pp. 264–277. [ Google Scholar ]
• Mokoena, M.P.; Chelule, P.K.; Gqaleni, N. Reduction of fumonisin B1 and zearalenone by lactic acid bacteria in fermented maize meal. J. Food Prot. 2005 , 68 , 2095–2099. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Rollan, G.C.; Gerez, C.L.; LeBlanc, J.G. Lactic fermentation as a strategy to improve the nutritional and functional values of pseudocereals. Front. Nutr. 2019 , 6 , 98. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Samtiya, M.; Aluko, R.E.; Dhewa, T. Plant food anti-nutritional factors and their reduction strategies: An overview. Food Prod. Process. Nutr. 2020 , 2 , 1–14. [ Google Scholar ] [ CrossRef ]
• Hill, D.; Sugrue, I.; Arendt, E.; Hill, C.; Stanton, C.; Ross, R.P. Recent advances in microbial fermentation for dairy and health. F1000Research 2017 , 6 . [ Google Scholar ] [ CrossRef ]
• Gupta, R.K.; Gangoliya, S.S.; Singh, N.K. Reduction of phytic acid and enhancement of bioavailable micronutrients in food grains. J. Food Sci. Technol. 2015 , 52 , 676–684. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Jesch, E.D.; Carr, T.P. Food ingredients that inhibit cholesterol absorption. Prev. Nutr. Food Sci. 2017 , 22 , 67. [ Google Scholar ] [ CrossRef ]
• Minh, N.G. Investigation of pickled water spinach (Ipomoea aquatic) fermentation by Lactobacillus sp. Int. J. Multidiscip. Res. Dev. 2014 , 1 , 71–80. [ Google Scholar ]
• Chadare, F.J.; Idohou, R.; Nago, E.; Affonfere, M.; Agossadou, J.; Fassinou, T.K.; Kenou, C.; Honfo, S.; Azokpota, P.; Linnemann, A.R.; et al. Conventional and food-to-food fortification: An appraisal of past practices and lessons learned. Food Sci. Nutr. 2019 , 7 , 2781–2795. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Wiley, K.D.; Gupta, M. Vitamin B1 thiamine deficiency (Beriberi). In StatPearls [Internet] ; Stat Pearls Publishing: Treasure Island, FL, USA, 2019. [ Google Scholar ]
• Barennes, H.; Sengkhamyong, K.; Rene, J.P.; Phimmasane, M. Beriberi (thiamine deficiency) and high infant mortality in northern Laos. PLoS Negl. Trop. Dis. 2015 , 9 , e0003581. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Law, S.V.; Abu Bakar, F.; Mat Hashim, D.; Abdul Hamid, A. Popular fermented foods and beverages in Southeast Asia. Int. Food Res. J. 2011 , 18 , 475–484. [ Google Scholar ]
• Nout, M.J.R.; Kiers, J.L. Tempe fermentation, innovation, and functionality: Update into the third millenium. J. Appl. Microbiol. 2005 , 98 , 789–805. [ Google Scholar ] [ CrossRef ]
• Ghosh, D.; Chattopadhyay, P. Preparation of idli batter, its properties, and nutritional improvement during fermentation. J. Food Sci. Technol. 2011 , 48 , 610–615. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Escalante, A.; Lopez Soto, D.R.; Velazquez Gutierrez, J.E.; Giles-Gomez, M.; Bolivar, F.; Lopez-Munguia, A. Pulque, a traditional Mexican alcoholic fermented beverage: Historical, microbiological, and technical aspects. Front. Microbiol. 2016 , 7 , 1026. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Escalante, A.; Giles-Gomez, M.; Flores, G.E.; Acuña, V.M.; Moreno-Terrazas, R.; Lopez-Munguia, A.; Lappe-Oliveras, P. Pulque fermentation. In Handbook of Plant-Based Fermented Food and Beverage Technology ; CRC Press: Boca Raton, FL, USA, 2012; pp. 691–706. [ Google Scholar ]
• Tamang, J.P.; Cotter, P.D.; Endo, A.; Han, N.S.; Kort, R.; Liu, S.Q.; Mayo, B.; Westerik, N.; Hutkins, R. Fermented foods in a global age: East meets West. Compr. Rev. Food Sci. Food Saf. 2020 , 19 , 184–217. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Aka, S.; Konan, G.; Fokou, G.; Dje, K.M.; Bonfoh, B. Review of African traditional cereal beverages. Am. J. Res. Commun. 2014 , 2 , 103–153. [ Google Scholar ]
• Amoa-Awua, W.K.; Sampson, E.; Tano-Debrah, K. Growth of yeasts, lactic, and acetic acid bacteria in palm wine during tapping and fermentation from felled oil palm ( Elaeis guineensis ) in Ghana. J. Appl. Microbiol. 2007 , 102 , 599–606. [ Google Scholar ] [ CrossRef ]
• Karamoko, D.; Moroh, J.L.A.; Bouatenin, K.M.J.P.; Dje, K.M. Biochemical and microbial properties of palm wine: Effect of tapping length and varietal differences. Food Nutr. Sci. 2016 , 7 , 763–771. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Anal, A.K. Quality ingredients and safety concerns for traditional fermented foods and beverages from Asia: A review. Fermentation 2019 , 5 , 8. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Liu, C.F.; Pan, T.M. In vitro effects of lactic acid bacteria on cancer cell viability and antioxidant activity. J. Food Drug Anal. 2010 , 18 , 77–86. [ Google Scholar ]
• Abubakar, M.A.S.; Hassan, Z.; Imdakim, M.M.A.; Sharifah, N.R.S.A. Antioxidant activity of lactic acid bacteria (L.A.B.) fermented skim milk as determined by 1,1-diphenyl-2-picrylhydrazyl (D.P.P.H.) and ferrous chelating activity (F.C.A.). Afr. J. Microbiol. Res. 2012 , 6 , 6358–6364. [ Google Scholar ] [ CrossRef ]
• Chettri, R.; Tamang, J.P. Functional properties of Tungrymbai and Bekang, naturally fermented soybean foods of North East India. Int. J. Fermented Foods 2014 , 3 , 87–103. [ Google Scholar ] [ CrossRef ]
• Moktan, B.; Saha, J.; Sarkar, P.K. Antioxidant activities of soybean as affected by Bacillus -fermentation to kinema . Food Res. Int. 2008 , 41 , 586–593. [ Google Scholar ] [ CrossRef ]
• Tamang, J.P. Naturally fermented ethnic soybean foods of India. J. Ethn. Foods 2015 , 2 , 8–17. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Astuti, M.N.; Suparmo, M.; Soesatyo, H.N.E. The role of black soybean tempe in increasing antioxidant enzyme activity and human lymphocyte proliferation in vivo. Int. J. Curr. Microbiol. Appl. Sci. 2013 , 2 , 316–327. [ Google Scholar ]
• Shon, M.Y.; Lee, J.; Choi, J.H.; Choi, S.Y.; Nam, S.H.; Seo, K.I.; Lee, S.W.; Sung, N.J.; Park, S.K. Antioxidant and free radical scavenging activity of methanol extract of chungkukjang. J. Food Compost. Anal. 2007 , 20 , 113–118. [ Google Scholar ] [ CrossRef ]
• Shin, D.; Jeong, D. Korean traditional fermented soybean products: Jang. J. Ethn. Foods 2015 , 2 , 2–7. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Dajanta, K.; Janpum, P.; Leksing, W. Antioxidant capacities, total phenolics, and flavonoids in black and yellow soybeans fermented by Bacillus subtilis : A comparative study of Thai fermented soybeans (thuanao). Int. Food Res. J. 2013 , 20 , 3125. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Ping, P.; Shih, C.; Rong, T.; King, Q. Effect of isoflavone aglycone content and antioxidation activity in natto by various cultures of Bacillus subtilis during the fermentation period. J. Nutr. Food Sci. 2012 , 2 , 153. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Wang, L.J.; Li, D.; Zou, L.; Dong Chen, X.; Cheng, Y.Q.; Yamaki, K.; Li, L.T. Antioxidative activity of douchi (a Chinese traditional salt-fermented soybean food) extracts during its processing. Int. J. Food Prop. 2007 , 10 , 385–396. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Farvin, K.S.; Baron, C.P.; Nielsen, N.S.; Jacobsen, C. Antioxidant activity of yoghurt peptides: Part 1- in vitro assays and evaluation in ω-3 enriched milk. Food Chem. 2010 , 123 , 1081–1089. [ Google Scholar ] [ CrossRef ]
• Park, J.M.; Shin, J.H.; Gu, J.G.; Yoon, S.J.; Song, J.C.; Jeon, W.M.; Suh, H.J.; Chang, U.J.; Yang, C.Y.; Kim, J.M. Effect of antioxidant activity in kimchi during a short-term and over-ripening fermentation period. J. Biosci. Bioeng. 2011 , 112 , 356–359. [ Google Scholar ] [ CrossRef ]
• Zhang, Y.; Hu, P.; Lou, L. Antioxidant activities of lactic acid bacteria for quality improvement of fermented sausage: Antioxidant activities of lactic acid bacteria. J. Food Sci. 2017 , 82 , 2960–2967. [ Google Scholar ] [ CrossRef ]
• De Mejia, E.G.; Dia, V.P. The role of nutraceutical proteins and peptides in apoptosis, angiogenesis, and metastasis of cancer cells. Cancer Metast. Rev. 2010 , 29 , 511–528. [ Google Scholar ] [ CrossRef ]
• Nagai, T.; Tamang, J.P. Fermented Soybeans Non-soybeans legumes foods. In Fermented Foods and Beverages of the World ; Tamang, J.P., Kailasapathy, K., Eds.; CRC Press: New York, NY, USA, 2010; pp. 191–224. [ Google Scholar ]
• Phelan, M.; Kerins, D. The potential role of milk-derived peptides in cardiovascular disease. Food Funct. 2011 , 2 , 153–167. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Hou, J.C.; Liu, F.; Ren, D.X.; Han, W.W.; Du, Y.O. Effect of culturing conditions on the expression of key enzymes in the proteolytic system of Lactobacillus bulgaricus . J. Zhejiang Univ. Sci. 2015 , 16 , 317–326. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Alcantara, C.; Bauerl, C.; Revilla-Guarinos, A.; Perez-Martinez, G.; Monedero, V.; Zuniga, M. Peptide and amino acid metabolism is controlled by an OmpR-family response regulator in Lactobacillus casei . Mol. Microbiol. 2016 , 100 , 25–41. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Vukotic, G.; Strahinic, I.; Begovic, J.; Lukic, J.; Kojic, M.; Fira, D. Survey on proteolytic activity and diversity of proteinase genes in mesophilic lactobacilli. Microbiology 2016 , 85 , 33–41. [ Google Scholar ] [ CrossRef ]
• Griffiths, M.W.; Tellez, A.M. Lactobacillus helveticus : The proteolytic system. Front. Microbiol. 2013 , 4 , 30. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Miyamoto, M.; Ueno, H.M.; Watanabe, M.; Tatsuma, Y.; Seto, Y.; Miyamoto, T. Distinctive proteolytic activity of cell envelope proteinase of Lactobacillus helveticus isolated from airag, a traditional Mongolian fermented mare’s milk. Int. J. Food Microbiol. 2015 , 197 , 65–71. [ Google Scholar ] [ CrossRef ]
• Stefanovic, E.; Fitzgerald, G.; McAuliffe, O. Advances in the genomics and metabolomics of dairy lactobacilli: A review. Food Microbiol. 2017 , 61 , 33–49. [ Google Scholar ] [ CrossRef ]
• Singh, T.A.; Devi, K.R.; Ahmed, G.; Jeyaram, K. Microbial and endogenous origin of fibrinolytic activity in traditional fermented foods of Northeast India. Food Res. Int. 2014 , 55 , 356–362. [ Google Scholar ] [ CrossRef ]
• Qian, B.; Xing, M.; Cui, L.; Deng, Y.; Xu, Y.; Huang, M.; Zhang, S. Antioxidant, antihypertensive, and immunomodulatory activities of peptide fractions from fermented skim milk with Lactobacillus delbrueckii subsp. bulgaricus LB340. J. Dairy Res. 2011 , 78 , 72. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Chen, Y.; Wang, Z.; Chen, X.; Liu, Y.; Zhang, H.; Sun, T. Identification of angiotensin I-converting enzyme inhibitory peptides from koumiss, a traditional fermented mare’s milk. J. Dairy Sci. 2010 , 93 , 884–892. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Quiros, A.; Hernández-Ledesma, B.; Ramos, M.; Amigo, L.; Recio, I. Angiotensin-converting enzyme inhibitory activity of peptides derived from caprine kefir. J. Dairy Sci. 2005 , 88 , 3480–3487. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Papadimitriou, K.; Alegria, A.; Bron, P.A.; De Angelis, M.; Gobbetti, M.; Kleerebezem, M.; Lemos, J.A.; Linares, D.M.; Ross, P.; Stanton, C.; et al. Stress physiology of lactic acid bacteria. Microbiol. Mol. Biol. Res. 2016 , 80 , 837–890. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Meyer, J.; Butikofer, U.; Walther, B.; Wechsler, D.; Sieber, R. Hot topic: Changes in angiotensin-converting enzyme inhibition and concentrations of the tripeptides Val-Pro-Pro and Ile-Pro-Pro during ripening of different Swiss cheese varieties. J. Dairy Sci. 2009 , 92 , 826–836. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Moslehishad, M.; Ehsani, M.R.; Salami, M.; Mirdamadi, S.; Ezzatpanah, H.; Naslaji, A.N.; Moosavi-Movahedi, A.A. The comparative assessment of ACE-inhibitory and antioxidant activities of peptide fractions obtained from fermented camel and bovine milk by Lactobacillus rhamnosus PTCC 1637. Int. Dairy J. 2013 , 29 , 82–87. [ Google Scholar ] [ CrossRef ]
• Ichimura, T.; Hu, J.; Aita, D.Q.; Maruyama, S. Angiotensin I-converting enzyme inhibitory activity and insulin secretion stimulative activity of fermented fish sauce. J. Biosci. Bioeng. 2003 , 96 , 496–499. [ Google Scholar ] [ CrossRef ]
• Sanjukta, S.; Rai, A.K. Production of bioactive peptides during soybean fermentation and their potential health benefits. Trends Food Sci. Technol. 2016 , 50 , 1–10. [ Google Scholar ] [ CrossRef ]
• Nout, M.J.R.; Aidoo, K.E. Asian fungal fermented food. In Industrial Applications ; Springer: Berlin/Heidelberg, Germany, 2002; pp. 23–47. [ Google Scholar ] [ CrossRef ]
• Suganuma, T.; Fujita, K.; Kitahara, K. Some distinguishable properties between acid-stable and neutral types of α-amylases from acid-producing koji. J. Biosci. Bioeng. 2007 , 104 , 353–362. [ Google Scholar ] [ CrossRef ]
• Tamang, J.P.; Dewan, S.; Tamang, B.; Rai, A.; Schillinger, U.; Holzapfel, W.H. Lactic acid bacteria in hamei and marcha of North East India. Indian J. Microbiol. 2007 , 47 , 119–125. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Tsuyoshi, N.; Fudou, R.; Yamanaka, S.; Kozaki, M.; Tamang, N.; Thapa, S.; Tamang, J.P. Identification of yeast strains isolated from marcha in Sikkim, a microbial starter for amylolytic fermentation. Int. J. Food Microbiol. 2005 , 99 , 135–146. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Mine, Y.; Wong, A.H.K.; Jiang, B. Fibrinolytic enzymes in Asian traditional fermented foods. Food Res. Int. 2005 , 38 , 243–250. [ Google Scholar ] [ CrossRef ]
• Kotb, E. Fibrinolytic bacterial enzymes with thrombolytic activity. In Fibrinolytic Bacterial Enzymes with Thrombolytic Activity ; Springer: Berlin/Heidelberg, Germany, 2012; pp. 1–74. [ Google Scholar ] [ CrossRef ]
• Chang, C.T.; Wang, P.M.; Hung, Y.F.; Chung, Y.C. Purification and biochemical properties of a fibrinolytic enzyme from Bacillus subtilis -fermented red bean. Food Chem. 2012 , 133 , 1611–1617. [ Google Scholar ] [ CrossRef ]
• Zeng, W.; Li, W.; Shu, L.; Yi, J.; Chen, G.; Liang, Z. Non-sterilized fermentative co-production of poly (γ-glutamic acid) and fibrinolytic enzyme by a thermophilic Bacillus subtilis GXA-28. Bioresour. Technol. 2013 , 142 , 697–700. [ Google Scholar ] [ CrossRef ]
• Montriwong, A.; Rodtong, S.; Yongsawatdigul, J. Detergent-stable salt-activated proteinases from Virgibacillus halodenitrificans SK1-3-7 isolated from fish sauce fermentation. Appl. Biochem. Biotechnol. 2015 , 176 , 505–517. [ Google Scholar ] [ CrossRef ]
• Vitale, D.C.; Piazza, C.; Melilli, B.; Drago, F.; Salomone, S. Isoflavones: Estrogenic activity, biological effect, and bioavailability. Eur. J. Drug Metab. Pharmacokinet. 2013 , 38 , 15–25. [ Google Scholar ] [ CrossRef ]
• Chiou, R.Y.Y.; Cheng, S.L. Isoflavone transformation during soybean koji preparation and subsequent miso fermentation supplemented with ethanol and NaCl. J. Agric. Food Chem. 2001 , 49 , 3656–3660. [ Google Scholar ] [ CrossRef ]
• Wang, L.J.; Yin, L.J.; Li, D.; Zou, L.; Saito, M.; Tatsumi, E. Influences of processing and NaCl supplementation on isoflavone contents and composition during douchi manufacturing. Food Chem. 2007 , 101 , 1247–1253. [ Google Scholar ] [ CrossRef ]
• Lee, Y.W.; Kim, J.D.; Zheng, J.; Row, K.H. Comparisons of isoflavones from Korean and Chinese soybean and processed products. Biochem. Eng. J. 2007 , 36 , 49–53. [ Google Scholar ] [ CrossRef ]
• Lu, Y.; Wang, W.; Shan, Y.; Zhi-Qiang, E.; Wang, L.Q. Study on the inhibition of fermented soybean to cancer cells. J. Northeast. Agric. Univ. (Engl. Ed.) 2009 , 16 , 25–28. [ Google Scholar ]
• Nakajima, N.; Nozaki, N.; Ishihara, K.; Ishikawa, A.; Tsuji, H. Analysis of isoflavone content in tempeh, a fermented soybean, and preparation of new isoflavone-enriched tempeh. J. Biosci. Bioeng. 2005 , 100 , 685–687. [ Google Scholar ] [ CrossRef ]
• Kwak, C.S.; Park, S.C.; Song, K.Y. Doenjang, a fermented soybean paste, decreased visceral fat accumulation and adipocyte size in rats fed with a high-fat diet more effectively than non-fermented soybeans. J. Med. Food 2012 , 15 , 1–9. [ Google Scholar ] [ CrossRef ]
• Paucar-Menacho, L.M.; Amaya-Farfan, J.; Berhow, M.A.; Mandarino, J.M.G.; de Mejia, E.G.; Chang, Y.K. A high-protein soybean cultivar contains lower isoflavones and saponins but higher minerals and bioactive peptides than a low-protein cultivar. Food Chem. 2010 , 120 , 15–21. [ Google Scholar ] [ CrossRef ]
• Ellington, A.A.; Berhow, M.A.; Singletary, K.W. Inhibition of Akt signaling and enhanced ERK1/2 activity are involved in the induction of macroautophagy by triterpenoid B-group soyasaponins in colon cancer cells. Carcinogenesis 2006 , 27 , 298–306. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Ishii, Y.; Tanizawa, H. Effects of soyasaponins on lipid peroxidation through the secretion of thyroid hormones. Biol. Pharm. Bull. 2006 , 29 , 1759–1763. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Murata, M.; Hodai, T.; Yamamoto, H.; Matsumori, N.; Oishi, T. Membrane interaction of soyasaponins in association with their antioxidation effect-Analysis of biomembrane interaction. Soy Prot. Res. 2006 , 9 , 82–86. [ Google Scholar ]
• Yanagisawa, Y.; Sumi, H. Natto Bacillus contains a large amount of water-soluble vitamin K (menaquinone-7). J. Food Biochem. 2005 , 29 , 267–277. [ Google Scholar ] [ CrossRef ]
• Omizu, Y.; Tsukaoto, C.; Chettri, R.; Tamang, J.P. Determination of saponin contents in raw soybean and fermented soybean foods of India. J. Sci. Ind. Res. India 2011 , 70 , 533–538. [ Google Scholar ]
• Meerak, J.; Iida, H.; Watanabe, Y.; Miyashita, M.; Sato, H.; Nakagawa, Y.; Tahara, Y. Phylogeny of γ-polyglutamic acid-producing Bacillus strains isolated from fermented soybean foods manufactured in Asian countries. J. Gen. Appl. Microbiol. 2007 , 53 , 315–323. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Nishito, Y.; Osana, Y.; Hachiya, T.; Popendorf, K.; Toyoda, A.; Fujiyama, A.; Itaya, M.; Sakakibara, Y. A whole-genome assembly of a natto production strain Bacillus subtilis from very short read data. BMC Genom. 2010 , 11 , 243. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Stanley-Wall, N.; Lazazzera, B.A. Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly--dl-glutamic acid production and biofilm formation. Mol. Microbiol. 2005 , 57 , 1143–1158. [ Google Scholar ] [ CrossRef ]
• Oppermann-Sanio, F.B.; Steinbüchel, A. Occurrence, functions and biosynthesis of polyamides in microorganisms and biotechnological production. Naturwissenschaften 2002 , 89 , 11–22. [ Google Scholar ] [ CrossRef ]
• Yoon, S.H.; Do, J.H.; Lee, S.Y.; Chang, H.N. Production of poly-γ-glutamic acid by fed-batch culture of Bacillus licheniformis . Biotechnol. Lett. 2000 , 22 , 585–588. [ Google Scholar ] [ CrossRef ]
• Tamang, J.P.; Shin, D.H.; Jung, S.J.; Chae, S.W. Functional properties of microorganisms in fermented foods. Front. Microbiol. 2016 , 7 , 578. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Omolara, B.O. Cyanide content of commercial gari from different areas of Ekiti State, Nigeria. World J. Nutr. Health 2014 , 2 , 58–60. [ Google Scholar ] [ CrossRef ]
• Lambri, M.; Fumi, M.D.; Roda, A.; De Faveri, D.M. Improved processing methods to reduce the total cyanide content of cassava roots from Burundi. Afr. J. Biotechnol. 2013 , 12 . [ Google Scholar ] [ CrossRef ]
• Bamidele, O.P.; Fasogbon, M.B.; Oladiran, D.A.; Akande, E.O. Nutritional composition of fufu analog flour produced from Cassava root ( Manihot esculenta ) and Cocoyam ( Colocasia esculenta ) tuber. Food Sci. Nutr. 2015 , 3 , 597–603. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Sanchez, P.C. Philippine Fermented Foods: Principles and Technology ; UP Press: Quezon City, Philippines, 2008. [ Google Scholar ]
• Laskowski, W.; Gorska-Warsewicz, H.; Rejman, K.; Czeczotko, M.; Zwolinska, J. How important are cereals and cereal products in the average polish diet? Nutrients 2019 , 11 , 679. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Verni, M.; Rizzello, C.G.; Coda, R. Fermentation biotechnology applied to cereal industry by-products: Nutritional and functional insights. Front. Nutr. 2019 , 6 , 42. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Erkmen, O.; Bozoglu, T.F. Fermented cereal and grain products. In Food Microbiology: Principles into Practice ; John Wiley & Sons, Ltd.: Hoboken, NJ, USA, 2016. [ Google Scholar ] [ CrossRef ]
• Singh, A.K.; Rehal, J.; Kaur, A.; Jyot, G. Enhancement of attributes of cereals by germination and fermentation: A review. Crit. Rev. Food Sci. Nutr. 2015 , 55 , 1575–1589. [ Google Scholar ] [ CrossRef ]
• Mariod, A.A.; Idris, Y.M.; Osman, N.M.; Mohamed, M.A.; Sukrab, A.M.; Farag, M.Y.; Matthaus, B. Three Sudanese sorghum-based fermented foods (kisra, hulu-mur, and abreh): Comparison of proximate, nutritional value, microbiological load, and acrylamide content. Ukr. J. Food Sci. 2016 , 4 , 216–228. [ Google Scholar ] [ CrossRef ]
• Walker, G.M.; Stewart, G.G. Saccharomyces cerevisiae in the production of fermented beverages. Beverages 2016 , 2 , 30. [ Google Scholar ] [ CrossRef ]
• Rezac, S.; Kok, C.R.; Heermann, M.; Hutkins, R. Fermented foods as a dietary source of live organisms. Front. Microbiol. 2018 , 9 , 1785. [ Google Scholar ] [ CrossRef ]
• Liptakova, D.; Matejcekova, Z.; Valik, L. Lactic acid bacteria and fermentation of cereals and pseudocereals. Fermen. Proc. 2017 , 10 , 65459. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Aguirre, M.; Collins, M.D. Lactic acid bacteria and human clinical infection. J. Appl. Bacteriol. 1993 , 75 , 95–107. [ Google Scholar ] [ CrossRef ]
• Garneau, J.E.; Moineau, S. Bacteriophages of lactic acid bacteria and their impact on milk fermentations. Microb. Cell Factories 2011 , 10 , S20, BioMed Central. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Aragon, F.; Perdigon, G.; de LeBlanc, A.D.M. Modification in the diet can induce beneficial effects against breast cancer. World J. Clin. Oncol. 2014 , 5 , 455. [ Google Scholar ] [ CrossRef ]
• Hagan, N.D.; Tabe, L.M.; Molvig, L.; Higgins, T.J.V. Modifying the amino acid composition of grains using gene technology. In Plant Biotechnology 2002 and Beyond ; Springer: Dordrecht, The Netherlands, 2003; pp. 305–308. [ Google Scholar ] [ CrossRef ]
• Biji, K.B.; Ravishankar, C.N.; Venkateswarlu, R.; Mohan, C.O.; Gopal, T.S. Biogenic amines in seafood: A review. Int. J. Food Sci. Technol. 2016 , 53 , 2210–2218. [ Google Scholar ] [ CrossRef ]
• Ruiz-Capillas, C.; Herrero, A.M. Impact of biogenic amines on food quality and safety. Foods 2019 , 8 , 62. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Durak-Dados, A.; Michalski, M.; Osek, J. Histamine and other biogenic amines in food. J. Vet. Res. 2020 , 64 , 281–288. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Penas, E.; Martinez-Villaluenga, C.; Frias, J. Sauerkraut: Production, composition, and health benefits. In Fermented Foods in Health and Disease Prevention ; Academic Press: Cambridge, MA, USA, 2017; pp. 557–576. [ Google Scholar ] [ CrossRef ]
• Kalac, P.; Spicka, J.; Krizek, M.; Pelikanova, T. The effects of lactic acid bacteria inoculants on biogenic amines formation in sauerkraut. Food Chem. 2000 , 70 , 355–359. [ Google Scholar ] [ CrossRef ]
• Karovicova, J.; Kohajdova, Z. Lactic acid fermented vegetable juices. HortSci (Pargue) 2003 , 30 , 152–158. [ Google Scholar ]
• Kalac, P.; Spicka, J.; Krizek, M.; Pelikanova, T. Changes in biogenic amine concentrations during sauerkraut storage. Food Chem. 2000 , 69 , 309–314. [ Google Scholar ] [ CrossRef ]
• Kirschbaum, J.; Rebscher, K.; Brückner, H. Liquid chromatographic determination of biogenic amines in fermented foods after derivatization with 3, 5-dinitrobenzoyl chloride. J. Chromatogr. A 2000 , 881 , 517–530. [ Google Scholar ] [ CrossRef ]
• Hornero-Mendez, D.; Garrido-Fernandez, A. Rapid high-performance liquid chromatography analysis of biogenic amines in fermented vegetable brines. J. Food Prot. 1997 , 60 , 414–419. [ Google Scholar ] [ CrossRef ]
• Kolesarova, E. Vyskyt a vznik biogennych aminov v potravinach. Bull. PV 1995 , 34 , 109–122. [ Google Scholar ]
• Mehta, B.M. Chemical composition of milk and milk products. In Handbook of Food Chemistry ; Springer: Berlin/Heidelberg, Germany, 2015; pp. 511–553. [ Google Scholar ]
• Shiby, V.K.; Mishra, H.N. Fermented milk and milk products as functional foods—A review. Crit. Rev. Food Sci. Nutr. 2013 , 53 , 482–496. [ Google Scholar ] [ CrossRef ]
• Hao, W.; Tian, P.; Zheng, M.; Wang, H.; Xu, C. Characteristics of proteolytic microorganisms and their effects on proteolysis in total mixed ration silages of soybean curd residue. Asian Austral. J. Anim. 2020 , 33 , 100. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Savijoki, K.; Ingmer, H.; Varmanen, P. Proteolytic systems of lactic acid bacteria. Appl. Microbiol. Biotechnol. 2006 , 71 , 394–406. [ Google Scholar ] [ CrossRef ]
• Dutra Rosolen, M.; Gennari, A.; Volpato, G.; Volken de Souza, C.F. Lactose hydrolysis in milk and dairy whey using microbial β-galactosidases. Enzym. Res. 2015 , 2015 . [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Ye, A.; Cui, J.; Dalgleish, D.; Singh, H. Effect of homogenization and heat treatment on the behavior of protein and fat globules during gastric digestion of milk. J. Dairy Sci. 2017 , 100 , 36–47. [ Google Scholar ] [ CrossRef ]
• Yoshii, K.; Hosomi, K.; Sawane, K.; Kunisawa, J. Metabolism of dietary and microbial vitamin B family in the regulation of host immunity. Front. Nutr. 2019 , 6 , 48. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Vieco-Saiz, N.; Belguesmia, Y.; Raspoet, R.; Auclair, E.; Gancel, F.; Kempf, I.; Drider, D. Benefits and inputs from lactic acid bacteria and their bacteriocins as alternatives to antibiotic growth promoters during food-animal production. Front. Microbiol. 2019 , 10 , 57. [ Google Scholar ] [ CrossRef ] [ PubMed ] [ Green Version ]
• Garcia-Burgos, M.; Moreno-Fernandez, J.; Alferez, M.J.; Diaz-Castro, J.; Lopez-Aliaga, I. New perspectives in fermented dairy products and their health relevance. J. Funct. Foods 2020 , 72 , 104059. [ Google Scholar ] [ CrossRef ]
• Bintsis, T. Lactic acid bacteria as starter cultures: An update in their metabolism and genetics. AIMS Microbiol. 2018 , 4 , 665. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Mastanjevic, K.; Kovacevic, D.; Frece, J.; Markov, K.; Pleadin, J. The effect of autochthonous starter culture, sugars, and temperature on the fermentation of Slavonian Kulen. Food Technol. Biotechnol. 2017 , 55 , 67–76. [ Google Scholar ] [ CrossRef ]
• Papagianni, M. Metabolic engineering of lactic acid bacteria for the production of industrially important compounds. Comput. Struct. Biotechnol. 2012 , 3 , e201210003. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Dalcanton, F.; Carrasco, E.; Perez-Rodríguez, F.; Posada-Izquierdo, G.D.; Falcao de Aragao, G.M.; Garcia-Gimeno, R.M. Modeling the combined effects of temperature, pH, and sodium chloride and sodium lactate concentrations on the growth rate of Lactobacillus plantarum ATCC 8014. J. Food Qual. 2018 . [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Juturu, V.; Wu, J.C. Microbial production of lactic acid: The latest development. Crit. Rev. Biotechnol. 2016 , 36 , 967–977. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Fadda, S.; Vignolo, G.; Oliver, G. Meat protein degradation by tissue and lactic acid bacteria enzymes. In Food Microbiology Protocols ; Humana Press: Totova, NJ, USA, 2001; pp. 147–162. [ Google Scholar ] [ CrossRef ]
• Toldrá, F. The role of muscle enzymes in dry-cured meat products with different drying conditions. Trends Food Sci. Technol. 2006 , 17 , 164–168. [ Google Scholar ] [ CrossRef ]
• Pasini, F.; Soglia, F.; Petracci, M.; Caboni, M.F.; Marziali, S.; Montanari, C.; Gardini, F.; Grazia, L.; Tabanelli, G. Effect of fermentation with different lactic acid bacteria starter cultures on biogenic amine content and ripening patterns in dry fermented sausages. Nutrients 2018 , 10 , 1497. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Karslioglu, B.; Cicek, U.; Kolsarici, N.; Candogan, K. Lipolytic changes in fermented sausages produced with Turkey meat: Effects of starter culture and heat treatment. Korean J. Food Sci. Anim. Resour. 2014 , 34 , 40–48. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Gianelli, M.P.; Salazar, V.; Mojica, L.; Friz, M. Volatile compounds present in traditional meat products (charqui and longaiza sausage) in Chile. Braz. Arch. Biol. Technol. 2012 , 55 , 603–612. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Kosowska, M.; Majcher, M.A.; Fortuna, T. Volatile compounds in meat and meat products. Food Sci. Technol. 2017 , 37 , 1–7. [ Google Scholar ] [ CrossRef ] [ Green Version ]
• Erginkaya, Z. Determination of organic acids in fermented sausage. Gida 1993 , 18 , 373–376. [ Google Scholar ]
• Kasankala, L.M.; Xiong, Y.L.; Chen, J. Enzymatic activity and flavor compound production in fermented silver carp fish paste inoculated with a douchi starter culture. J. Agric. Food Chem. 2012 , 60 , 226–233. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Demeyer, D.; Raemaekers, M.; Rizzo, A.; Holck, A.; De Smedt, A.; Ten Brink, B.; Hagen, B.; Montel, C.; Zanardi, E.; Murbrekk, E.; et al. Control of bioflavour and safety in fermented sausages: First results of a European project. Food Res. Int. 2000 , 33 , 171–180. [ Google Scholar ] [ CrossRef ]

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Sharma, R.; Garg, P.; Kumar, P.; Bhatia, S.K.; Kulshrestha, S. Microbial Fermentation and Its Role in Quality Improvement of Fermented Foods. Fermentation 2020 , 6 , 106. https://doi.org/10.3390/fermentation6040106

Sharma R, Garg P, Kumar P, Bhatia SK, Kulshrestha S. Microbial Fermentation and Its Role in Quality Improvement of Fermented Foods. Fermentation . 2020; 6(4):106. https://doi.org/10.3390/fermentation6040106

Sharma, Ranjana, Prakrati Garg, Pradeep Kumar, Shashi Kant Bhatia, and Saurabh Kulshrestha. 2020. "Microbial Fermentation and Its Role in Quality Improvement of Fermented Foods" Fermentation 6, no. 4: 106. https://doi.org/10.3390/fermentation6040106

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Challenges in coffee fermentation technologies: bibliometric analysis and critical review

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• Published: 02 September 2024

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• Valeria Hurtado Cortés   nAff1 ,
• Andrés Felipe Bahamón Monje   ORCID: orcid.org/0000-0002-2620-148X 1 ,
• Jaime Daniel Bustos Vanegas   nAff1 &
• Nelson Gutiérrez Guzmán   nAff1  

Advancements in coffee processing technologies have led to improved efficiency in field operations, but challenges still exist in their practical implementation. Various alternatives and solutions have been proposed to enhance processing efficiency and address issues related to safety, standardization, and quality improvement in coffee production. A literature review using SciMAT and ScientoPy software highlighted advancements in fermentation tanks and the emergence of novel fermentation methodologies. However, these innovations lack sufficient scientific evidence. Researchers are now focusing on systematic approaches, such as controlled fermentations and evaluating the influence of microorganisms and process conditions on sensory attributes and coffee composition. Brazil is the leader in coffee bean fermentation research, but the number of published papers in the field has recently decreased. Despite this, efforts continue to improve process control and optimize product quality. The study emphasizes the need for further innovation in coffee fermentation technologies to increase efficiency, sustainability, and profitability while minimizing environmental impact. Implementing these advancements promises a more sustainable and quality-driven future for the coffee industry.

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Introduction

Coffee is a crucial agricultural product and a popular beverage globally. Its growing popularity has led to the need for improved processes to enhance cup quality. The coffee fruit, also known as almond or green coffee, is composed of five layers that protect the endosperm. These layers, known as pulp, mucilage, parchment, and epidermis, form the endosperm and are subjected to roasting to form the flavor and aroma of the coffee drink.

The processing of coffee fruit involves stages to preserve the quality of the almond, which is then subjected to roasting. The types of processing include dry, semi-dry, and wet (de Melo Pereira et al. 2015 ). Dry processing involves pulping, fermentation, washing, drying, threshing, and roasting. Semi-dry processing involves mechanical removal of the exocarp and part of the mucilage, while wet processing involves drying and threshing.

Green coffee, obtained after processing, varies according to agro-climatological characteristics, species, variety, processing type, and post-harvest operations. Control of these operations is essential to preserve grain quality and maintain the consistency of its sensory profile.

Coffee fermentation is a metabolic process that converts sugars into energy and compounds through the action of enzymes in mucilage (Silva et al. 2013 ). This process involves the pulped coffee mass being kept in closed containers for 12 to 72 h to remove the mesocarp (mucilage) attached to the parchment. The mucilage, composed of simple sugars and a pectic substrate, is degraded into alcohols and organic acids by microorganisms, such as yeasts and bacteria (Correa et al. 2014 ; Pereira et al. 2016b ).

Coffee fermentation is a metabolic process that converts sugars into energy and compounds through the action of enzymes in mucilage. This process involves the pulped coffee mass being kept in closed containers for 12 to 72 h to remove the mesocarp (mucilage) attached to the parchment. The mucilage, composed of simple sugars and a pectic substrate, is degraded into alcohols and organic acids by microorganisms, such as yeasts and bacteria (Bressani et al. 2021b ).

Metabolites diffuse through parchment and endosperm, potentially causing exosmosis during fermentation until chemical potential equilibrium is achieved. The decrease in pH causes mucilage degradation, which can be removed by washing with water. Controlled fermentation can produce beverages with special aromas and flavors, such as sweet, citrus, and fruity.

Mucilage removal can be performed using mechanical or enzymatic methods, such as mechanical abrasion in ELMU-type mucilage removal machines and enzymes like Ultrazym 100, Irgazim 100, Benefax, and Cofepec. Recent research has revealed that the microbial degradation process during fermentation leads to physical and chemical changes in almonds, impacting the sensory characteristics of the resulting drink (da Mota et al. 2020 ; Elhalis et al. 2021 ).

Factors affecting reaction rates during coffee fermentation include temperature, water availability, fermentation time, and fruit maturity index. Devices designed for the operation must allow control and measurement of these factors to standardize the process.

This article shows the advances achieved over time with the technologies and methods used in the fermentation of coffee, taking into account the improvement in the processes of safety, standardization and quality of coffee. A bibliographic analysis of research focused on technologies and representative authors with related publications, among other aspects, was carried out. All with the purpose of observing the progress in the fermentation process with the objective of continuing researching and looking for solutions to obtain efficient and quality processing.

Search methodology

A bibliometric analysis was conducted on coffee bean fermentation publications to identify trends, emerging research directions, and relationships with fermenters and process variables, using Scopus database and ScientoPy and SciMAT software.

Databases, keywords and search criteria

This study analyzed data from the Scopus database on coffee, bean, and fermentation from 2001 to 2022, focusing on top countries, document types, and institutions, and downloaded in .CSV format for ScientoPy and SciMAT software.

Analysis using ScientoPy software

The downloaded data from Scopus were then loaded and processed with ScientoPy and the pre-processing results are presented in Table  1 . The journals and keywords categories were analyzed with the software to know the most relevant issues, total documents published by journal and keywords and evolution of them in the period from 2001 to 2022.

Analysis using SciMAT software

The data was preprocessed in modules “Knowledge base” and “Group sets” to remove duplicates and related keywords. The analysis was set to three periods (2001–2017, 2018–2020, and 2021–2022) and parameters were selected in “Analysis” to create evolution maps, strategic diagrams, and clusters.

Search results

Trends in publications over time.

The search for 231 documents from 2001 to 2022 revealed a stable trend in published documents. Between 2012 and 2022, there was a decrease in publications (Fig.  1 A and B). The top five countries were Brazil, followed by Indonesia, China, South Korea, and Colombia (Fig.  1 C). The majority of documents were articles, with a small percentage of reviews. The Universidade Federal de Lavras leads the list with 26 publications on the search topic, followed by Brazilian Universidade Federal do Parana (Fig.  1 -D). Indonesian institutions Hasanuddin University and Universitas Sylah Kuala also appear in the top 10. Nestlé S.A. ranks sixth in the top ten.

Documents published in the search topic (Graphs extracted from Scopus online database). ( A ) Documents published by year ( B ) Documents published by type ( C ) Documents published by country ( D ) Documents published by institution

There is no clear trend in the number of publications in the top 10 journals over time. Food Research International and IOP Conference Series: Earth and Environmental Science had the largest publications in 2020 and 2021 respectively. The evolution of the top 10 keywords is showed in Fig.  2 . This graph corroborates the main terms used and shows an increase over time of this words. After “Coffee”, which is a general term, “Fermentation” term has the highest number of documents published in the period analyzed, but according to the percentage of documents published in the last year 2021–2022 graph, “coffee fermentation” had the highest value (42.1%) in comparison to the other terms, which indicates that in the last year, this topic has had a higher relative growth.

Keywords in research related to the search topic ( A ) Cloud diagram of the top 1000 words ( B ) Evolution graph of the top 10 words

Although in general the interest in the fermentation process of coffee remains constantly growing, the topics addressed are diverse, which can be evidenced in the variety of key terms that the search throws up. Figure  2 -A shows the cloud of words specifically related to the fermentation process, such as types of fermentation, process control, variables involved, and fermenters. In relation to the latter, only two specific terms about it appear in the cloud, “bioreactors” and “bioreactor”; and some terms related with variables, control process or devices such as “controlled fermentation”, “temperature distribution”, ohmic technology”, “ohmic heating”.

Besides, some differences are obtained with the processing of data in SciMAT (Table  2 ), since this tool allows groups conformations in similar words and documents not related with the topic, however, words like “Fermentation” and “Coffee” remains as main terms, which is expected since these are general terms. Respect to the journals, the results are similar with some exceptions.

Topic evolution map and strategic diagram and cluster’s network

Figure  3 shows the graphs generated by SciMAT from the analysis of the data associated with the search string. According to the evolution map (Figs.  3 -1), for period 2001–2017 it can be observed nine main terms: “bacteria”, “coffee aroma”, “metabolomics”, “arabica”, “fungal fermentations”, “beverages”, “microorganisms”, “types of fermentation”, and “coffee”. In the period 2018–2020, the number of relevant terms increase to eleven, and only “microorganisms”, “coffee” and “type of fermentation” terms remain. New terms are included such as “classification”, “genetics”, “bacillus”, “yeast”, “seeds”, “sensory analysis” and “volatiles”. With respect to period 2020–2022, “bioreactors and process variables” term appears for the first time and there are new terms, for instance, analytical techniques as “spectrometry” and “chromatography”.

( 1 ) Evolution map of the relevant terms regarding the search topic in the documents reported from 2001 to 2022, and relevant relationships on evolution map. The color lines represent the main associations found, and ( 2 ) Strategic diagram associated with topic of interest for period ( A ) 2001–2017, ( B ) 2018–2020, ( C ) 2021–2022. ( 3 ) Cluster of terms associated with topic of interest for period ( A ) 2001–2017, ( B ) 2018–2020, ( C ) 2021–2022

With respect to the relevant associations shown on the evolution map (Figs.  3 -1), it is possible to observe terms associated with the study of microorganisms (relationships highlighted in red), such as bacteria, especially of the genus Bacillus, fungal fermentation, mainly related to yeasts, and lactic acid fermentation. These terms, in turn, present associations with parameters such as sensory analysis and volatiles. The latter is related to “bioreactor and process variables” in the last period. The term “bioreactor and process variables” is backward associated with “coffee”, a general term, and “types of fermentation”, which, in turn, is associated with “coffee aroma” (relationships highlighted in blue). These associations are anticipated due to the disparate processing methodologies, where the conditions of the process, the utilization of starter cultures, the type of microorganisms employed, and the generation of organic acids that contribute to alterations in the volatile and aroma profiles of roasted coffee are implicated (da Mota et al. 2020 ). Additionally the control of process variable offered by bioreactors has recently shown to contribute to the production of coffee with higher sensory quality and reproducibility (de Carvalho Neto et al. 2018 ).

The strategic diagrams and cluster networks for each period are presented in Fig.  3 (2) and (3). The volume of the spheres is proportional to the number of published documents associated with each theme. The upper-right quadrant is motor-themes, with terms in the upper-left quadrant being highly development and isolated themes. The lower-left quadrant is emerging or declining themes, while the lower-right quadrant is transversal and general. In the first period, “beverages”, “metabolomics”, and “fungal fermentation” are motor themes, while “types of fermentation” is an emergent theme. In the second period, “types of fermentation” remains an emergent theme, with “yeast” added to this category. In the third period, “coffee” is less frequent, with more specific topics such as “bacillus”, “genetics”, and “classification” as motor themes (Elhalis et al. 2021 ). For the period 2020–2022, “volatiles” and “metabolomics” are motor themes, related to research on volatiles and metobolites generated in process fermentation (Elhalis et al. 2021 ; Prakash et al. 2022 ). “Types of fermentation” and “coffee” are tranversal themes, while “lactic acid fermentation” is an emergent theme. “Bioreactors and process variables” is an isolated theme for this period.

Figure  3 (3) displays clusters of terms related to bioreactors and process variables control. The volume of spheres is proportional to the number of documents corresponding to each keyword, and the thickness of the link between two spheres is proportional to the equivalence index between these words. For the period 2001–2017, “bioreactor and process variables” is slightly related to “microorganisms”, “drying process”, “plant seed”, and “mucilage”. For the second period, “volatile” term shows a slight relationship with “bioreactor and process variables”, which in turn is associated with “coffee beans”. The main associations with “bioreactor and process variables” may be with “microorganisms” and “volatile”.

As regards the period 2021–2022 (Figs.  3 - (3) -C), strong bonds are observed between “Bioreactor and process variables”, “Food supply” and “Agriculture”, since the fermentation process is usually on-farm process, although efforts have been made to the process control (Martinez et al. 2017 ; de Carvalho Neto et al. 2018 ). Slight associations are seen with more specific terms such as “Liquid media”, “Enzymes”, “UV-VIS-Spectrophotometry” and “Biochemical analysis”. These terms are directly related to the fermentation process and its monitoring, whereby those relationships are expected.

Coffee fermentation methodologies

Scientific publications related to coffee fermentation devices were searched in the Web of Science, Scopus, and Science Direct databases. Published patents, as well as devices developed by different companies in the sector, were also included in the review. The evolution and characteristics of the devices and their impact on the quality and sensory profile of the coffee were tabulated and summarized in tables.

Table  3 presents various methods for controlling coffee fermentation, focusing on temperature, processing time, and microorganism addition. These parameters affect the grain’s physical-chemical composition and sensory profile. Fermentation times range from 12 h to several days, with low temperatures slowing microbial kinetics and requiring several days for pH to reach 3.8. Mass transfer between mucilage and grain layers occurs mainly through diffusion, leading to more complex profiles in long-time fermentation.

Evolution of technologies for coffee fermentation

Coffee fermentation devices are containers that allow the product volume to be maintained under homogeneous conditions during the process. Fermentation can be done dry or submerged, with the latter ensuring that all grains are in contact with an equal volume of oxygen. Most producers follow this method for a more homogeneous fermentation. Initially, pulped coffee was fermented in vat-type tanks made of wood, cement, or brick, which were plastered or enameled with cement or covered with baked clay veneers. The floor was built with a slope of 6 to 8% and a width-to-height ratio of 1:1.5 to facilitate leachate drainage and product removal. The final processing time was determined based on producer experience, such as the hole and touch test, which is subjective and prone to errors.

Producers have noticed that fermentation under certain conditions can result in heterogeneous coffee products with sour and fermented flavors due to the difficulty in controlling process variables. To improve sanitary conditions, Cenicafé and other manufacturers have developed high-density polyethylene vat-type tanks, which are lightweight, easy to handle, and clean. Cenicafé in Colombia has successfully maintained a stabilized process with less washing water consumption using Ecomill ® technology in stainless steel and high-density polyethylene. These systems incorporate cylindrical fermentation tanks with inverted cone-shaped bases and 60° horizontal inclination, allowing coffee to flow out by gravity.

Widyotomo, S., and Yusi, Y. ( 2013 ) evaluated the fermentation of cherry coffee in a horizontal type fermenter with electrical resistance and agitation (Fig.  4 -4-A). Working at 50% capacity (20 kg/batch), temperatures between 20 and 40 °C and times between 6 and 18 h, the authors defined optimal operating conditions at 25 °C and 12 h of processing. In an attempt to remove the mucilage using low temperatures to reduce the consumption of washing water, Bressani et al. ( 2020 ) evaluated a cold fermenter prototype. Temperatures close to 2 °C managed to denature the structure of the mucilage and then it was removed mechanically (Fig.  4 -4-B). In Brazil, some private companies have developed commercial prototypes for fermentation control. The Palinialves company developed a rotating cylinder (Fig.  4 -4-C) with a galvanized sheet, steel or stainless steel structure with internal blades and rpm control for a homogeneous mix. The system is completely sealed and has a relief valve for pressure control and temperature sensors. Its maximum capacity is 10,000 L. The Campotech company with the support of Embrapa and the Instituto Federal do Sul de Minas, developed a device for the controlled fermentation of 1,250 L of cherry or pulped coffee. The device, in the form of a vertical cylinder and conical base, has a helical agitation and temperature control systems for heating or cooling the coffee mass (Fig.  4 -4-D).

( 1 ) Vat-type tank for fermentation of pulped coffee. ( 2 ) High-density polyethylene vat-type tanks for coffee fermentation. ( A ) Cenicafé ( B ) Rotoplast ® . ( 3 ) Fermentation tank in Ecomill ® Technology. ( A ) 1,000 to 1,500 kg load capacity. ( B ) 2,000 to 6,000 kg load capacity. ( 4 ) Closed systems for coffee fermentation. ( A ) Widyotomo, S., & Yusi, Y. 2013 , ( B ) Correa et al. 2014 , ( C ) Palinialves, ( D ) CampoTech – Jacu Digital

Final remarks

Colombia, with over a century of coffee production experience, has limited knowledge in developing innovative fermentation prototypes. The fermentation process for washed coffees was once considered unimportant, focusing only on removing mucilage to reduce drying time. This neglect of safety and quality has led to issues with materials like concrete, majolica, wood, and cement. Technological advances in the last decade have led to the use of safe materials like high-density polyethylene and stainless steel in fermenters. Prototype fermenters or bioreactors with variable control systems and mechanical agitation have been developed in countries like Peru, Brazil, Chile, Spain, Indonesia, and Colombia. However, these high-cost technologies remain inaccessible to most producers. The industry has developed solutions such as helical-type central agitators and rotating drums, both with high energy consumption. A strategy is being evaluated for mixing through the recirculation of leachate, which requires less energy than the entire coffee mass. However, the impact of this methodology on the process quality has not been scientifically evaluated (Widyotomo and Yusianto 2013 ).

Conclusions

A bibliometric analysis of the literature on coffee fermentation indicates a growing interest and progress in research and development of technologies to improve sensory quality, safety, efficiency, and sustainability. Improvements in fermentation tanks have been identified in terms of materials, designs, and the incorporation of accessories such as digital sensors. Innovations in fermentation methodologies and a more scientific approach by researchers in this field have also been observed.

Moreover, the analysis indicates that issues related to coffee bean fermentation are undergoing constant evolution, with Brazil emerging as a leading contributor in this field. Despite a decline in the number of published papers over the past three years, research is focused on the design of controlled fermentations and the evaluation of the influence of microorganisms and process conditions on the sensory quality and composition of coffee. Nevertheless, it is observed that prototypes designed to regulate process variables, such as agitation and temperature, are costly and may be inaccessible to small-scale producers.

Collectively, these findings indicate that the integration of innovative technologies, enhanced methodologies, and a rigorous scientific approach is transforming the coffee industry towards enhanced efficiency, safety, and sustainability, with the potential to benefit both producers and consumers globally.

Data availability

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Code availability

Batista da Mota MC, Batista NN, Dias DR, Schwan RF (2022) Impact of microbial self-induced anaerobiosis fermentation (SIAF) on coffee quality. Food Biosci 47. https://doi.org/10.1016/j.fbio.2022.101640

Bressani APP, Martinez SJ, Evangelista SR et al (2018) Characteristics of fermented coffee inoculated with yeast starter cultures using different inoculation methods. LWT - Food Sci Technol 92:212–219. https://doi.org/10.1016/j.lwt.2018.02.029

Article   CAS   Google Scholar  

Bressani APP, Martinez SJ, Sarmento ABI et al (2020) Organic acids produced during fermentation and sensory perception in specialty coffee using yeast starter culture. Food Res Int 128:108773. https://doi.org/10.1016/j.foodres.2019.108773

Article   CAS   PubMed   Google Scholar  

Bressani APP, Batista NN, Ferreira G et al (2021a) Characterization of bioactive, chemical, and sensory compounds from fermented coffees with different yeasts species. Food Res Int 150. https://doi.org/10.1016/j.foodres.2021.110755

Bressani APP, Martinez SJ, Sarmento ABI et al (2021b) Influence of yeast inoculation on the quality of fermented coffee (Coffea arabica var. Mundo Novo) processed by natural and pulped natural processes. Int J Food Microbiol 343. https://doi.org/10.1016/j.ijfoodmicro.2021.109107

Brioschi D Junior, Carvalho Guarçoni R, de Cássia Soares da Silva M et al (2021) Microbial fermentation affects sensorial, chemical, and microbial profile of coffee under carbonic maceration. Food Chem 342:128296. https://doi.org/10.1016/j.foodchem.2020.128296

Cassimiro DM, de Batista J, Fonseca NN HC, et al (2022) Coinoculation of lactic acid bacteria and yeasts increases the quality of wet fermented Arabica coffee. Int J Food Microbiol 369. https://doi.org/10.1016/j.ijfoodmicro.2022.109627

Correa EC, Jiménez-Ariza T, Díaz-Barcos V et al (2014) Advanced characterisation of a coffee fermenting tank by multi-distributed wireless sensors: spatial interpolation and phase space graphs. Food Bioproc Tech 7:3166–3174. https://doi.org/10.1007/s11947-014-1328-4

da Mota MCB, Batista NN, Rabelo MHS et al (2020) Influence of fermentation conditions on the sensorial quality of coffee inoculated with yeast. Food Res Int 136. https://doi.org/10.1016/j.foodres.2020.109482

de Carvalho Neto DP, de Melo Pereira GV, Finco AMO et al (2018) Efficient coffee beans mucilage layer removal using lactic acid fermentation in a stirred-tank bioreactor: kinetic, metabolic and sensorial studies. Food Biosci 26:80–87. https://doi.org/10.1016/j.fbio.2018.10.005

De Carvalho Neto DP, De Vinícius G, Finco AMO et al (2020) Microbiological, physicochemical and sensory studies of coffee beans fermentation conducted in a yeast bioreactor model. Food Biotechnol 34:172–192. https://doi.org/10.1080/08905436.2020.1746666

de Melo Pereira GV, Soccol VT, Pandey A et al (2014) Isolation, selection and evaluation of yeasts for use in fermentation of coffee beans by the wet process. Int J Food Microbiol 188:60–66. https://doi.org/10.1016/j.ijfoodmicro.2014.07.008

de Melo Pereira GV, Neto E, Soccol VT et al (2015) Conducting starter culture-controlled fermentations of coffee beans during on-farm wet processing: growth, metabolic analyses and sensorial effects. Food Res Int 75:348–356. https://doi.org/10.1016/j.foodres.2015.06.027

Elhalis H, Cox J, Frank D, Zhao J (2021) The role of wet fermentation in enhancing coffee flavor, aroma and sensory quality. Eur Food Res Technol 247:485–498. https://doi.org/10.1007/s00217-020-03641-6

Evangelista SR, da Cruz Pedrozo Miguel MG, de Souza Cordeiro C et al (2014) Inoculation of starter cultures in a semi-dry coffee (Coffea arabica) fermentation process. Food Microbiol 44:87–95. https://doi.org/10.1016/j.fm.2014.05.013

Evangelista SR, Miguel MG, da Silva CP CF, et al (2015) Microbiological diversity associated with the spontaneous wet method of coffee fermentation. Int J Food Microbiol 210:102–112. https://doi.org/10.1016/j.ijfoodmicro.2015.06.008

Fioresi DB, Pereira LL, Catarina da Silva Oliveira E et al (2021) Mid infrared spectroscopy for comparative analysis of fermented arabica and robusta coffee. Food Control 121. https://doi.org/10.1016/j.foodcont.2020.107625

Martinez SJ, Bressani APP, da Miguel MG CP, et al (2017) Different inoculation methods for semi-dry processed coffee using yeasts as starter cultures. Food Res Int 102:333–340. https://doi.org/10.1016/j.foodres.2017.09.096

Martins PMM, Ribeiro LS, Miguel MG da CP, et al (2019) Production of coffee (Coffea arabica) inoculated with yeasts: impact on quality. J Sci Food Agric 99:5638–5645. https://doi.org/10.1002/jsfa.9820

Martins PMM, Batista NN, da Miguel MG CP, et al (2020) Coffee growing altitude influences the microbiota, chemical compounds and the quality of fermented coffees. Food Res Int 129:108872. https://doi.org/10.1016/j.foodres.2019.108872

Partida-Sedas JG, Muñoz Ferreiro MN, Vázquez-Odériz ML et al (2019) Influence of the postharvest processing of the Garnica coffee variety on the sensory characteristics and overall acceptance of the beverage. J Sens Stud 34:1–12. https://doi.org/10.1111/joss.12502

Article   Google Scholar  

Pereira GV, de Carvalho Neto M, Medeiros DP ABP, et al (2016a) Potential of lactic acid bacteria to improve the fermentation and quality of coffee during on-farm processing. Int J Food Sci Technol 51:1689–1695. https://doi.org/10.1111/ijfs.13142

Pereira GVM, Soccol VT, Soccol CR (2016b) Current state of research on cocoa and coffee fermentations. Curr Opin Food Sci 7:50–57. https://doi.org/10.1016/j.cofs.2015.11.001

Prakash I, R SS, P SH, et al (2022) Metabolomics and volatile fingerprint of yeast fermented robusta coffee: a value added coffee. Lwt 154:112717. https://doi.org/10.1016/j.lwt.2021.112717

Pregolini VB, de Melo Pereira GV, da Silva Vale A et al (2021) Influence of environmental microbiota on the activity and metabolism of starter cultures used in coffee beans fermentation. Fermentation 7. https://doi.org/10.3390/fermentation7040278

Ribeiro LS, Ribeiro DE, Evangelista SR et al (2017) Controlled fermentation of semi-dry coffee (Coffea arabica) using starter cultures: a sensory perspective. LWT - Food Sci Technol 82:32–38. https://doi.org/10.1016/j.lwt.2017.04.008

Samaniego Rodriguez MA (2019) Evaluación de maceración carbónica y adición de levaduras (Saccharomyces cerevisiae) durante el lavado de café Geisha (Coffea arabica). Escuela Agrícola Panamericana 41

Silva CF, Vilela DM, de Souza Cordeiro C et al (2013) Evaluation of a potential starter culture for enhance quality of coffee fermentation. World J Microbiol Biotechnol 29:235–247. https://doi.org/10.1007/s11274-012-1175-2

Sulaiman I, Hasni D (2022) Microorganism growth profiles during fermentation of Gayo Arabica wine coffee. IOP Conf Ser Earth Environ Sci 951. https://doi.org/10.1088/1755-1315/951/1/012076

Widyotomo S, Yusianto D (2013) Optimizing of Arabica coffee bean fermentation process using a controlled fermentor. Pelita Perkebunan (a coffee and cocoa. Res Journal) 29:53–68. https://doi.org/10.22302/ICCRI.JUR.PELITAPERKEBUNAN.V29I1.191

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Project financed by the Ministry of Science and Technology of Colombia (Minciencias). Project of the General System of Royalties BPIN No. 2020000100460.

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Valeria Hurtado Cortés, Jaime Daniel Bustos Vanegas & Nelson Gutiérrez Guzmán

Present address: Facultad de Ingeniería, Grupo de Investigación Agroindustria USCO, Universidad Surcolombiana, Centro Surcolombiano de Investigación en Café – CESURCAFÉ, Avenida Pastrana Borrero Carrera 1a, Neiva, 410001, Huila, Colombia

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Cortés, V.H., Bahamón Monje, A.F., Bustos Vanegas, J.D. et al. Challenges in coffee fermentation technologies: bibliometric analysis and critical review. J Food Sci Technol (2024). https://doi.org/10.1007/s13197-024-06054-5

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Alternative food technology: Precision fermentation’s future in NZ explored in new discussion paper

Precision fermentation could significantly impact NZ's food production, particularly in the dairy sector. Photo / Mark Mitchell

The group behind a new discussion paper, Understanding Precision Fermentation , says it has been developed in response to growing interest from the Southland farming community.

Precision fermentation is a technology that could significantly impact New Zealand’s food production, particularly in the dairy sector.

The discussion paper, released by community-led group Thriving Southland, provides an accessible introduction to the technology, presents a range of stakeholder views, and directs readers to further detailed studies.

It draws on recently published research undertaken by others: it doesn’t present any new research undertaken by Thriving Southland.

Richard Kyte, project lead at Thriving Southland, said the paper was about “informing our community”.

“We’ve heard from farmers and stakeholders who want to know more about precision fermentation, and we’ve responded by providing a resource that provides an introductory overview of the technology, to encourage further discussion,” he said.

The paper emphasised that while the future impacts of precision fermentation remained uncertain, the time to start thinking about potential disruptions and opportunities was now.

It also highlighted that this resource was not a representation of Thriving Southland’s views but intended to inform and provoke thought within the community.

Anna Crosbie, the paper’s author, said the dairy sector was a cornerstone of Southland’s economy and contributed significantly to employment and regional output.

“With precision fermentation being widely regarded as the alternative protein technology most likely to impact New Zealand first, we wanted to help farmers access recent research and better understand how precision fermentation might impact us in the future.”

The discussion paper is funded by the Ministry of Business, Innovation and Employment through the Southland Just Transition initiative and is part of Thriving Southland’s ongoing efforts to explore future food and fibre opportunities for the region.

Key points from Understanding Precision Fermentation

Potential impact: Precision fermentation could reshape the dairy sector, offering new opportunities and presenting challenges that require strategic thinking and preparation. The scale and pace of disruption remains unknown - though more forecast scenarios are emerging.

Global investment: There is growing global investment in precision fermentation. New Zealand’s current regulatory environment may limit rapid growth in this area, making it crucial to enhance resilience against potential disruptions.

Debate on strategic direction: Opinions vary on how much New Zealand should invest now in preparing for potential disruptions brought by precision fermentation. The discussion paper highlights the importance of national and regional dialogues to determine the best path forward.

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