Kerala has quietly made history, with something really tiny. A microbe.
It recently became the first in India to officially declare a state microbe — the bacterium Bacillus subtilis. The announcement was made during the inauguration of the Centre of Excellence in Microbiome (CoEM) in Thiruvananthapuram.
Guided by the motto ‘Microbes for Life’, the centre will focus on how microorganisms influence sustainability, health and the environment. “The facility is the first organisation in India to unify microbiome-based translational research across human health, nutrition, agriculture, fisheries and environmental protection,” says CoEM director Sabu Thomas.
Unlike conventional research institutes that work in silos, CoEM studies microbes across domains — humans, animals, plants, aquatic systems and environmental media — to translate scientific knowledge into real-world benefits. “We will also provide a platform for young entrepreneurs to advance their research,” Sabu adds.
His team member and scientist, Karthika S, explains that CoEM operates through two specialised wings. “One focuses on interdisciplinary research and product development, while the other uses big data and AI for spatio-temporal mapping of microbiome data,” she says.
“Currently, the centre is guiding two startups — one focusing on soil microbiomes and another on microbes derived from fermented foods and biodegradable waste.”
The choice of Bacillus subtilis was far from symbolic. “A government-appointed committee of researchers, doctors and professors zeroed in on this microbe after extensive discussions,” says Sabu.
Naturally found in soil, water, the human gut and fermented foods, Bacillus subtilis is known for its resilience and safety. “In Kerala, its presence has been widely reported across unique landscapes, including mangrove forests, waterbodies and traditional fermented food items,” Sabu notes.
Its usefulness spans sectors. In agriculture, it functions as a bio-fertiliser that boosts crop yield and acts as a biocontrol agent against diseases. In industry, it is used for enzyme production. It plays a role in wastewater treatment and environmental purification too. Most importantly, it is a vital probiotic aiding human and animal health.
Beyond policy, Sabu believes the declaration carries a deeper message, especially in a post-pandemic world. “Not all microbes are harmful. There are microbes like Bacillus subtilis that are highly beneficial,” he smiles.
Why does this matter?
India already has a national microbe: Lactobacillus bulgaricus. And there have been several studies on the subject.
However, understanding friendly microbes at the common people’s level is increasingly vital, particularly for gut health.
Experts point out that the gut is often called the body’s ‘second brain’ because of its influence on physical and mental well-being. General physician Dr Satish Nayak says microbes like Bacillus subtilis play a role in managing chronic conditions such as irritable bowel syndrome (IBS), constipation and diarrhoea.
“Modern lifestyle — stress, poor diet and the overuse of antibiotics — destroy the essential bacteria our gut needs to function,” he says.
“While medical substitutes are available, natural sources like curd, yoghurt, buttermilk and the Japanese fermented food natto are excellent ways to keep these microbes flourishing.”
The gut’s link to the rest of the body is often underestimated, Dr Satish adds. He points to migraines as one overlooked example.
“The gut and brain are constantly communicating. When the gut microbiome — the ecosystem of microbes — is imbalanced, it can trigger inflammatory responses that affect the nervous system,” he explains, noting that youngsters are particularly vulnerable.
Studies underscore the concern. One report highlighted IBS prevalence of 12.27 per cent, linked not just to diet but also stress, anxiety and depression. A 2017 statewide survey found over 2,000 of 2,142 patients suffering from various forms of irritable bowel disease (IBD).
A 2025 study published in the ‘Journal of Family Medicine and Primary Care’, found 66.4 per cent prevalence of functional gastrointestinal disorders (FGIDs) among adults in Kerala.
Notably, the study suggested strengthening the existing healthcare system with ground-level programmes focusing on FGIDs and probiotics.
Recent research suggests that alterations in the gut microbiome may lead to increased risk of Parkinson’s disease. These findings point to a possible link between lifestyle-driven changes in gut flora and the development or progression of neurodegenerative diseases.
Wellness coach Rajiv Ambat welcomes the ‘state microbe’ declaration, noting that more awareness can help curb the worrying rise in gut-related issues among Malayalis. “Friendly gut microbes are crucial for proper absorption and assimilation of nutrients. When the microbiome is not at an optimal level, it affects the whole system — from head to toe,” he says.
“Intake of junk/processed food, alcohol consumption, smoking, odd food timings, excess caffeine, and irrational use of antibiotics take a toll on the gut microbiome. It’s a common pattern I see among many of my clients these days,” he says.
Rajiv, who is a lifestyle disorders researcher and founder of SOLVEMyHealth, points out that a deficiency of healthy gut microbes can even affect the hormonal balance of the body.
“One prime example is serotonin, aka the ‘happy hormone’. Studies have shown that poor gut health leads to a dip in serotonin levels, which can cause mood disorders,” he says.
“Moreover, gut microbiome imbalance leads to issues such as indigestion and bloating, which affect one’s productivity.”
Echoing the observations, clinical dietician Gayathri V notes that microbial imbalance is also linked to obesity and metabolic disorders. “Fermented milk drinks and kombucha, rich in beneficial bacteria, are now widely available. They support digestion and even weight management,” she says.
“It’s not just about probiotics. One has to ensure sufficient intake of fibre-rich food — prebiotics, or the fuel for healthy gut microbes. Holistic wellness lies in a simple mantra: balanced diet, proper hydration, and regular exercise.”
Power up with pazhankanji!
Fermentation boosts growth of healthy microbes in natural edible items. Besides the peppy tang to food and drink, the probiotic muscle of fermented food has held them in good stead for centuries.
The good-old pazhankanji, once frugal fare, is now increasingly recommended as a healthy breakfast.
Its recent claim to fame comes from Stanley Medical College, which stamped it as a superfood for gut health. Made with slighlty fermented batter, appam, idli and dosa are also top recommendations. No list is complete without brine pickles. Among drinks, sambharam or spiced buttermilk, perhaps, takes the numero uno spot.
It joins traditional fermented drinks across India:
-Kanji from the north (fermented beetroot and carrot in mustardy water)
-Tanka torani from the east (spiced, fermented rice water)
-Ambil from the west (millets fermented in buttermilk)
Curd is another probiotic bomb. In Kerala, it is central
to dishes such as pachadi, kichadi, inji-thairu, and pulissery. Curd also defines some regional versions of avial, especially in north Kerala.
Changing times have brought newer probiotic batches, like kombucha.
Closing in is tepache, brewed from pineapple skin fermented with jaggery and cinnamon. Many more — like sauerkraut, kefir and miso — are also trending.