Fermentation is the Story of How We Domesticated Microbes

There is no denying that fermentation has now evolved into a billion dollar industry but at its crux, it is the simple conversion of sugars by various microorganisms. Akhila Vijayaraghavan expands the story of fermentation, how it is deeply intertwined with the history of human civilization, and how in fact, we are what we eat.

The history of fermentation is deeply intertwined with the history of human civilisation.

Brewing beer can be traced back to 7000 BCE, to Ancient Egypt and the Sumerians. In Ancient India, dairy was fermented to produce yoghurt. In the Middle Ages, baking bread with a sourdough starter was fine-tuned. During the Renaissance, it was determined that wine fermentation was better controlled by use of a culture. In the 19th century, Louis Pasteur conclusively determined that yeast is responsible for alcoholic fermentation. In the early 20th century, this knowledge led to the rise of commercial breweries and wineries. Fermentation then spilled over to other aspects, including the production of penicillin in the late 20th century.

Sourdough starter. More on baking with starter and local grains here.

It is impossible to pinpoint the first person who was responsible for the process of fermentation. The closest documented case of intentional fermentation can be attributed to Zosimos of Panopolis (circa 300-400AD), an ancient Greek alchemist who lived in Egypt. However, it well could have been an undocumented caveman making fruit wine in the Rift Valley. There is no denying that fermentation has now evolved into a billion dollar industry but at its crux, it is the simple conversion of sugars by various microorganisms.

Yeasts, Bacteria, and Fungus: Creation and Flavour

Broadly speaking, fermentation of foods was carried out as a method of preservation, to enhance flavour and aroma, to make food more nutritious, and for the production of alcohol, and vinegar. Different types of microbes play different roles in achieving the final outcome.

In beer, the fermentative agent is yeast. Suryakant Singh, chief brewer at Catamaran Brewery in Pondicherry states that processes, temperatures, and methodology change the final outcome of the product. “Sugar is broken down into ethanol, carbon dioxide, as well as esters and phenolic compounds which add flavour. It is this flavour that is responsible for diversification in beer styles and is the difference between a Trappist beer and a stout”, he explains. “Beer brewing these days depends predominantly on commercial Brewer’s yeast (a cousin of Baker’s yeast). Brewing mead on the other hand, was the result of accidental fermentation of honey by wild yeasts.”

Mead is seeing a recent revival, with some artisanal mead-makers preferring to use wild fermentation. It is interesting to note that although mead is commonly associated with neolithic Europeans, the earliest surviving written record of mead is possibly the soma mentioned in the Rigveda.

Coffee bean fermentation. Read about the rise of robusta coffee here.

Coffee is another crop where fermentation plays a role in coaxing the flavours out of the bean. “From the time the coffee cherries are picked to when they are processed, some form of uncontrolled fermentation occurs”, says Viggnesh, a Chennai-based independent coffee researcher. “High-quality artisanal coffee is made by controlling this fermentation process and it plays a critical role in the final flavour and aroma of the coffee. This degree of control is what separates great coffee from decent coffee.” Chocolate goes through a similar process where the flavour of the final product only comes out when the cacao beans are fermented and then dried. Both of these rely on lacto-fermentation with bacteria rather than yeast.

Fermenting cacao beans. Read about India’s first cacao and craft chocolate festival here.

Some other ferments like sake, miso, and soy sauce depend on koji, a fungal inoculum, instead of bacteria. It is made by inoculating steamed grains, typically rice or barley, with spores of the fungus Aspergillus oryzae. Its use dates back to at least 300 BCE in China. Fungal inoculum is also used in cheese-making to produce mould-ripened cheeses with distinct flavours and provenance like Roquefort and Camembert.

DIY Fermentation

It is mind-boggling to realise that a handful of genuses of microbes are responsible for the disparate array of beverages and foods like mead, beer, whisky, wine, kombucha, tepeche, chaas, kanji, kvass, vinegar, yogurt, kefir, sour cream, skyr, sauerkraut, gundruk, kimchi, soy sauce, sochi, sake, tempeh, mirin, miso, appam, idli, dosa, dhokla, naan, mishit doi, shrikhand, kadhi, ghee, jalebis, certain cheeses, pickles, hákarl, salami, butter, buttermilk, ghee, sourdough, injera, garum, fish sauce, which all came into existence in that sweet spot between serendipity and the magic of science.

My guides to fermentation when I first started, was Payal Shah’s invaluable Instagram account, Kobo Fermentary, as well as The Noma Guide to Fermentation, and Sandor Katz’s bible The Art of Fermentation. Finding cultures for some of these proved to be challenging, and along the way, I discovered Posh Flavours. Alla Petukhova, a Russian living in Ghaziabad started a business around selling cultures targeted at home fermenters. “Throughout my life, fermented foods like sour cream, kefir, yogurt, aged cheeses, and pickled foods were wisdom-driven, old-fashioned culinary customs.” When she moved to India, the idea was to create an ecosystem to encourage people to experience the joy of fermentation. “We started with the cheesemaking kits, providing an all-in-one solution to make cheeses easily at home and eventually grew our range of cultures.”

The most captivating thing about fermentation is the awareness that you are working with something that is so alive. Even if you’re fermenting something for the very first time, you intuitively know to trust your sense of taste and smell. Every time I ferment, it feels that I’m standing firmly at this intoxicating confluence of culture, history, time, slow-food, science, and generational knowledge.

Fermentation and Gut Health

The gut-brain axis is a topic frequently discussed by health enthusiasts. With the surge in availability of probiotics in the market, there is a growing emphasis on consuming fermented foods as well. As more and more research reveals, having a robust gut microbiome is the answer to many modern ailments. There is evidence that having diverse gut flora improves digestion, fights inflammation, produces short chain fatty acids (SCFAs) that nourish the gut lining, improves metabolic health, and moderates our immune system. Although kombucha, sauerkraut, kimchi, kefir etc., have vital roles to play, getting adequate amounts of probiotics into your diet doesn’t have to be fancy.

Kanji or fermented rice from kerala. Read more here.

It would be amiss not to mention the humblest of all fermented foods, which is present all over India and Asian cultures in various avatars. It is cooked rice, wild-fermented overnight by adding water. The Bengalis call it poita bhat, in Odiya it is pakhala bhat, pazhaya sadam in Tamil, and chaddannam in Telugu. It is usually mixed with diced shallots, green chillies, salt, a little yoghurt and eaten as a midday meal, especially in the hot summer months. In Sri Lanka and Malaysia, it is eaten with fried fish or sambal to give it a spicy punch.

The process of fermentation not only reduces the glycaemic index of rice, it also creates colonies of thriving probiotic bacteria. When buttermilk or yogurt is added, it diversifies this variety. The shallots contain inulin, a fermentable fibre which reaches the colon undigested, thereby acting like a prebiotic which feeds the probiotic bacteria in the gut. This simple meal has a full circle of life going, with elegantly simple ingredients.

India has many varieties of indigenous vinegars. Read about them here.

Fermented Foods and Human Health

Looking at historical evidence and scientific studies on the properties of several fermented foods; not only do they enrich the gut microbiome; they also actively help us fight off infections. In 500 BCE, mouldy soybean curds were used by the Chinese as an antibiotic treatment for boils. This was the first documented use of fermented food as medicine. Lactic acid bacteria isolated from the commonly eaten kadhi in India showed antibacterial activity against several strains of harmful bacteria including S. aureus and E. coli. Similarly Rhizopus oligosporus in tempeh creates metabolites that allows it to outcompete other harmful moulds and bacteria like Aspergillus flavus and S. aureus respectively, even after its consumed.

Lactic Acid Bacteria (LAB) like Lactobacillus, Streptococcus, Enterococcus etc., Acetic Acid Bacteria (AAB) like Acetobacter, certain moulds like Aspergillus, Rhizopus, yeasts like Saccharomyces as well as other bacterial species like Bifidobacterium, Clostridium, Pseudomonas, etc. are typically the work-horses of any fermentation process. Many of these species are also found making up our gut microflora. Perhaps this overlap is not a coincidence at all, but a purposeful collaboration in the process of co-evolution over millennia; and that you are indeed what you eat.

Akhila Vijayaraghavan is a trained molecular biologist. Now, she runs an urban hydroponic farm focused on agritech innovations. Follow her on Instagram: @thebokehchaser

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