Fermentation is a food preservation technique that was deeply embedded in my upbringing, long before I was aware of it. Fermented vegetables were a regular presence at home, although yoghurt was not something I ate as a child. My mother often made what we called “sour cabbage soup,” a dish whose flavour I later realised was similar to sauerkraut, though prepared differently. The process involved boiling Chinese cabbage or celery and adding it to noodle soup, then leaving it to sit for one or two days. Over time, the broth became pleasantly sour and refreshing. There were various ways to use it in cooking, but my favourite was sour soup with noodles, a real delicacy on hot summer days that brought a sense of freshness.
In autumn, we harvested vegetables from the garden, including peppers, daikon radish, aubergine, Jerusalem artichoke, and carrots. Fermenting them helped extend their shelf life and helped us prepare for winter, when fresh produce was scarce. In hindsight, this type of imperceptible influence and everyday practice shaped my healthy relationship with real food. Even now, I enjoy spending time cooking from scratch and preparing pickled vegetables in my own kitchen.
As a child, I didn’t understand the science or health benefits behind fermentation. I simply noticed the changes: food softened, flavours deepened, and aromas shifted, sometimes becoming strong or “funky”. When fermentation failed, it was often because the ingredients or containers were not properly sterilised, a clear sign of spoilage. When it succeeds, fermentation is guided by invisible microorganisms that drive a delicate transformation. Beyond vegetables, many were part of my everyday food landscape: kombucha, soy sauce, soybean paste (doenjang), and spicy soybean paste (ssamjang), red chilli pastes (gochujang), all common ingredients in Asian grocery stores. As I have travelled, I have come to appreciate the breadth of fermentation traditions worldwide.
Fermented foods in history and culture
The use of microbes in food fermentation dates back thousands of years; archaeological evidence suggests that fermented beverages such as rice wine were produced in China as early as 7000 BC, while bread and beer were staples in ancient Egypt. The genomics of isolates painted the evidence that the domestication of the yeast from far East Asia/China was transported to other regions through the Silk Road.
Yeasts such as Saccharomyces cerevisiae are key to alcohol production and were once considered safer to consume than untreated water, particularly during the industrial revolution in 18th century England. In 1857, Louis Pasteur demonstrated that fermentation was a biological process and established the central role of yeast in alcoholic fermentation. More than a century later, in 1996, scientists completed the genome sequence of the yeast Saccharomyces cerevisiae, making it the first eukaryotic organism to be fully sequenced. The yeast genome contains approximately 60000 genes and around one third of which are related to human genes. This discovery underscored how deeply intertwined humans and microbial biology are, revealing an evolutionary relationship that has continually shaped the adaptations of both microbes and their hosts.
In Europe, lactic acid bacteria play a similarly central role in fermented dairy products such as cheese and yoghurt. Common LAB genera include Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Streptococcus, alongside Bifidobacterium species in certain products. These microbes have been selectively cultivated over centuries, giving rise to region-specific textures, flavours, and production methods.
Alongside industrially produced fermented foods, many communities maintain indigenous fermentation practices using local ingredients such as cereals, legumes, fish, and meat. Often described as ethnic fermented foods, these products reflect deep cultural knowledge passed down through generations and remain distinct from mainstream cuisines. In South Korea, kimchi refers not to a single dish but to a diverse family of fermented vegetables. Alongside the widely known fermented Chinese cabbage (baechu-kimchi), there are many other varieties, including kkakdugi (cubed radish kimchi), oi sobagi (stuffed cucumber kimchi), pa-kimchi made from Korean green onions and etc. There also exists the World Institute of Kimchi, a dedicated research centre focused on its microbiology, nutrition, and industrial development.
Among the different types of kimchi, baechu-kimchi is the most globally recognised and widely consumed. The kimchi microbiome has been well characterised and is dominated by lactic acid bacteria (LAB), including species such as Lactobacillus plantarum, Leuconostoc mesenteroides, and Weissella koreensis. Kimchi fermentation typically occurs spontaneously and can be carried out at home without the addition of starter cultures. Interestingly, many of the LAB that drive fermentation originate not from the cabbage itself, but from seasoning ingredients such as garlic, ginger, leek, and red pepper powder. Variations in these ingredients influence microbial succession, shaping the final flavour, aroma, and texture of the product. This explains how homemade kimchi can taste markedly different from industrially produced.
Taken altogether, these practices showcase that fermentation is a truly universal practice. It has evolved and been woven as part of human civilisation. Fermented foods embody the ingenuity and wisdom of our ancestors, and still remain an indispensable part of everyday life shared across countries, cultures, and continents.
Health benefits
Fermentation is not driven by bacteria alone. Yeast and moulds also play essential roles. Together, these microorganisms sustain their own growth through chemical reactions that break down food components - notably, by converting sugars into organic acids that lower pH and inhibit the growth of pathogenic species. As a result, fermented food contains numerous bioactive compounds, including peptides and vitamins that are absent or scarce in raw ingredients. Fermentation also breaks down large, complex carbohydrates that are difficult for humans to digest, improving nutrient accessibility and absorption in the gut. Through these processes, fermentation often makes foods easier to digest and nutritionally more beneficial for us.
The benefits and risks of fermentation must be considered together. Growing scientific evidence suggests that including certain fermented foods in the diet may support health, with potential benefits such as reduced inflammation, enhanced immune function, and a lower risk of chronic diseases. However, not all fermentation is beneficial. Spontaneous fermentation relies on autochthonous (naturally occurring) microorganisms, which can create unique flavours but may also allow spoilage microbes to grow if poorly controlled.
A recent consumer recall involving SMA infant formula and follow-on formula from Nestlé, as well as a batch of Aptamil products from Danone, was triggered by concerns over the potential presence of the toxin cereulide, that is produced by strains of Bacillus cereus and other species. Cereulide disrupts mitochondrial function, damages cells, and can activate 5-HT3 serotonin receptors in the gut, causing symptoms such as vomiting, nausea and abdominal cramps. Subsequent investigation identified arachidonic acid (ARA) from an unnamed supplier as a likely source of contamination. ARA is made from microbial fermentation (Mortierella sect. schmuckeri) and added to baby formula to more closely mimic the lipid composition of human breast milk. The international infant formula recall set off alarms for both the food industry and regulators, promoting renewed attention on food safety surveillance systems. In response, the European Food Safety Authority (EFSA) developed the first guidance to safeguard the assessment of food for infants and other groups.
“Modern approaches such as precision fermentation use carefully selected or engineered microorganisms to produce specific food ingredients.” According to Yong Quan Tan, a scientist at the Singapore Food Agency. While this allows greater consistency and control, it also raises questions about safety, allergenicity, and long-term health effects, highlighting the need for careful regulation.
Fermented foods as probiotics
Fermented foods have attracted growing attention from nutritionists, clinicians, and consumers as research continues to uncover the health-promoting effects of selected fermented foods. However, it is important to distinguish between “fermented foods” and “probiotic fermented foods” – the two terms are not interchangeable. Not all fermented foods contain probiotics, and not all probiotic claims are supported by scientific evidence.
Probiotic fermented foods must meet specific criteria: they require strain-specific evidence of health benefit, confirmed safety, and presence of adequate numbers of live microorganisms in the final product to deliver the claimed effect. Critically, the microbes must remain viable at the time of consumption. Well-known examples include Lacticaseibacillus casei subsp. shirota, which is prominent in the Japanese sweetened probiotic milk beverage Yakult, and Lactobacillus delbrueckii subsp. bulgaricus, a primary starter culture used in yoghurt and cheese. Numerous other probiotic species have also been identified. Research indicates that probiotics may help reduce antibiotic-associated diarrhoea, with proposed mechanisms including increased production of short-chain fatty acids (SCFAs), modulation of bile acid metabolism, enhancement of gut barrier integrity, and suppression of opportunistic pathogens.
The health-promoting properties of probiotics have attracted substantial interest from the food industry. In particular, the rapid rise of glucagon-like peptide-1(GLP-1)–based anti-obesity and weight-management drugs has fueled enthusiasm for GLP-1–targeted functional foods. Among emerging candidates, Akkermansia muciniphila is considered a “next-generation” probiotic due to its strong association with improved gut barrier function and metabolic health. For example, it produces the membrane protein Amuc_1100, which enhances tight junction expression and strengthens the intestinal barrier, as well as protein G9, which stimulates GLP-1 secretion, promoting satiety and improved metabolic regulation.
Recent industry developments highlight this growing interest. Danone’s acquisition of The Akkermansia Company (TAC) – founded by scientists who first characterised Akkermansia muciniphila MucT® - underscores the commercial potential of this microorganism. Notably, A. muciniphila derivatives are being explored as postbiotics, defined by the International Scientific Association of Probiotics and Prebiotics (ISAPP) as Postbiotics offer advantages over traditional probiotics and prebiotics, including improved safety, stability, and ease of incorporation into food products, contributing to their considerable market potential.
Although the probiotic market is crowded with supplements and bold health claims, some of which can be misleading, certain probiotic strains have been proven to be effective in treating irritable bowel syndrome (IBS). IBS is a relapsing functional gastrointestinal disorder that affects the digestive system, and is a common gastrointestinal disorder in the clinic. According to the British Society of Gastroenterology guidelines, selected probiotics may provide symptom relief in some patients, although effects are strain-specific and not universal. Unlike supplements, probiotic fermented foods are still foods, but they are held to higher standards than conventional fermented foods. While fermented foods are not required to declare or characterise their microbial composition, probiotic fermented foods must demonstrate the presence and viability of specific beneficial strains. In practice, some fermented foods still contain live cultures, while others are pasteurised and no longer contain active microorganisms.
Food fermentation and gut microbial fermentation are distinct processes; food fermentation occurs outside the body under more controlled or semi-controlled conditions, whereas gut fermentation is carried out in vivo by the commensal microbiota within a highly individualised intestinal environment. Fermentation during food processing can improve digestibility, increase nutrient bioavailability, and enhance absorption. However, the presence of these properties does not automatically translate into health benefits for every consumer; outcomes depend on the type of fermented food, individual physiology, and the composition and functionality of the person’s existing gut microbiota.
For some individuals, particularly those with irritable bowel syndrome (IBS), certain fermented foods may exacerbate symptoms. In such cases, symptom management may involve a low-FODMAP diet, which restricts fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs). Some fermented products also contain live microorganisms that can interact with the gut microbiota. Nevertheless, the viability and functional impact of these microbes can be variable: many food-derived microorganisms may pass through the gastrointestinal tract transiently rather than colonizing long-term, and responses differ substantially between individuals. Any potential benefits are therefore more likely to depend on regular, sustained consumption as part of an overall balanced dietary pattern. Where appropriate, individuals should seek professional guidance when incorporating probiotic fermented foods into their diet or using probiotics as an adjunct or alternative approach for gut problems.
Further reading
https://link.springer.com/chapter/10.1007/978-981-10-2621-8_4
https://www.frontiersin.org/journals/nutrition/articles/10.3389/fnut.2025.1677478/full
https://www.mdpi.com/2311-5637/3/4/49
https://www.mdpi.com/2311-5637/3/4/49#fermentation-03-00049-t006
https://www.sciencedirect.com/science/article/pii/S107599641100206X?via%3Dihub
https://www.sciencedirect.com/science/article/pii/S0308814620303435?via%3Dihub/
https://www.theakkermansiacompany.com/blogs/news/the-akkermansia-company-is-acquired-by-danone
https://ift.onlinelibrary.wiley.com/doi/full/10.1111/1750-3841.12948
https://www.bbc.co.uk/news/articles/c1lz2m02rzzo
https://www.efsa.europa.eu/en/topics/topic/foods-infants-and-other-groups
https://pmc.ncbi.nlm.nih.gov/articles/PMC6043522/
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