Scientists discover 14 new gut bacteria species in Indian tribal communities

An NCCS Pune study uncovers nearly 200 previously undocumented microbial strains, showing that a healthy gut is shaped by diet, geography and lifestyle and why India needs its own microbiome map

4 min readAug 5, 2026 08:01 AM IST

The gut microbiome is the vast community of bacteria, fungi, viruses and other microorganisms that live in the human intestine. (Representational Image: Pixabay/Gerd Altmann/geralt)

Scientists at BRIC–National Centre for Cell Science (NCCS), Pune, have identified 14 previously unknown bacterial species and nearly 200 local microbial strains while studying the gut microbiomes of India’s tribal communities, highlighting how much of the country’s microbial diversity remains unexplored.

The findings, published in the journal Gut Microbes, challenge the idea of a universal “healthy” gut microbiome. Instead, they show that the microbes living in our intestines are shaped by where we live, what we eat and the communities we belong to.

The researchers say the study also raises important questions about relying solely on microbiome reference data — and even probiotics—developed in Western populations.

What is the gut microbiome?

The gut microbiome is the vast community of bacteria, fungi, viruses and other microorganisms that live in the human intestine. Together, they help digest food, regulate the immune system, protect the intestinal lining and prevent harmful microbes from growing.

“The gut microbiome differs from person to person and is influenced by diet, geography, medicines, environment and cultural practices,” said Dr Dhiraj Dhotre, scientist at BRIC-NCCS and co-corresponding author of the study.

The study analysed gut microbiomes from eight tribal communities across India — Warli from the western coast; Gond and Madia from the Deccan Plateau; Kabui (Rongmei Naga) from the Northeast Hills; and Boto, Balti, Brokpa and Purigpa from the Trans-Himalayan region.

According to Dr Yogesh Shouche, senior microbiome scientist and co-author, finding so many previously undocumented microbes in a relatively small study suggests that India’s microbiome remains a largely unexplored biological resource.

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No single blueprint for a healthy gut

Despite living in different regions, all eight communities shared three dominant bacterial groups — Segatella, Agathobacter and Faecalibacterium. However, the Indian strains of Segatella belonged to distinct genetic lineages not commonly represented in microbiome databases from Europe and North America.

“This tells us that an Indian gut microbiome should not be labelled abnormal simply because it differs from Western reference populations,” Dr Dhotre said. “Instead, we need population-specific microbiome data to understand what is healthy in different communities.”

Diet leaves a microbial signature

The greatest differences were seen in the four trans-Himalayan communities, whose traditional diets include milk, homemade butter, wheat and barley, along with rice and other plant-based foods such as leafy vegetables, tubers, fruits and berries.

These communities showed greater gut bacterial diversity and significantly higher levels of Bifidobacterium than tribes consuming little or no dairy. Their gut microbes also carried more genes involved in digesting lactose, galactose and grain-derived carbohydrates, suggesting that the microbiome adapts over generations to local dietary patterns.

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The researchers caution, however, that the study identifies strong associations rather than proving that dairy alone caused the differences. Larger, long-term studies will be needed to establish cause and effect.

What the findings mean for probiotics

One of the study’s key findings involved Bifidobacterium adolescentis, a bacterium widely used in probiotic research. The Indian strains differed genetically from those found in industrialised countries and carried a distinct set of carbohydrate-processing enzymes, indicating adaptation to local diets.

According to Dr Dhotre, the findings raise legitimate questions about the indiscriminate use of imported probiotics. However, they do not suggest that imported probiotics are ineffective or that Indian strains are necessarily superior. Instead, they underscore the need to evaluate probiotics in the context of local populations and dietary habits.

Why India needs its own microbiome map

The researchers say the discovery of new bacterial species and hundreds of previously undocumented strains is a reminder that India’s microbial diversity is still largely unmapped.

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Building an India-specific microbiome database could improve future research on nutrition, metabolic diseases and personalised medicine, while helping develop probiotics and dietary interventions that are better suited to Indian populations rather than relying exclusively on Western reference data.

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Anuradha Mascarenhas

Anuradha Mascarenhas is a Senior Editor at The Indian Express, based in Pune. With a career spanning three decades, she is one of the most respected voices in Indian journalism regarding healthcare, science and environment and research developments. She also takes a keen interest in covering women's issues . Professional Background Education: A gold medalist in Communication and Journalism from Savitribai Phule Pune University and a Master’s degree in Literature. Author: She authored the biography At The Wheel Of Research, which chronicles the life and work of Dr. Soumya Swaminathan, the former Chief Scientist at the WHO. Key Focus: She combines scientific accuracy with storytelling, translating complex medical research into compelling public and human-interest narratives. Awards and Recognition Anuradha has won several awards including the Press Council of India's national award for excellence in journalism under the gender based reporting category in 2019 and the Laadli Media award (gender sensitivity -2024). A recipient of the Lokmat journalism award (gender category-2022), she was also shortlisted for the RedInk awards for excellence in journalism-2021. Her debut book At The Wheel Of Research, an exclusive biography of Dr Soumya Swaminathan the inaugural chief scientist of World Health Organisation was also nominated in the Popular Choice Category of JK Paper AUTHER awards. She has also secured competitive fellowships including the Laadli Media Fellowship (2022), the Survivors Against TB – New Research in TB Media Fellowship (2023) and is part of the prestigious 2025 India Cohort of the WomenLift Health Leadership Journey.” Recent Notable Articles (Late 2025) 1. Cancer & Specialized Medical Care "Tata Memorial finds way to kill drug-resistant cancer cells" (Nov 26, 2025): Reporting on a breakthrough for triple-negative breast cancer, one of the most aggressive forms of the disease. Discipline, diet and purpose; How a 97-year-old professor defies ageing'' (Nov 15, 2025) Report about Prof Gururaj Mutalik, the first Head of Department at Pune's B J Government Medical College who at 97 credits his longevity to healthy habits and a strong sense of purpose. 2. Environmental Health (The "Breathless Pune" Series) Long-term exposure even to 'moderate' air leads to chronic heart, lung, kidney issues" (Nov 26, 2025): Part of an investigative series highlighting that even "safe" pollution levels are damaging to vital organs. "For every 10 µg/m3 increase in PM2.5 level, there was 6-8% jump in medicine sales" (Nov 23, 2025): Using commercial data to prove the direct link between air quality and respiratory illnesses in Pune. 3. Lifestyle & Wellness News "They didn't let cancer, diabetes and heart disease stop them from travelling" (Dec 22, 2025): A collaborative piece featuring survivors who share practical tips for traveling with chronic conditions. At 17, his BP shot up to 200/120 mmHG; Lancet study flags why child and teen hypertension doubled between 2000 and 2020'' (Nov 12,2025)--A report that focusses on 17-year-old-boy's hypertensive crisis and reflects the rising global trend of high blood pressure among children and adolescents. 4. Scientific Recognition & Infrastructure For promoting sci-comm, gender diversity: IUCAA woman prof highlighted in Nature" (Nov 25, 2025): Covering the global recognition of Indian women scientists in gender studies and physics. Pune researchers find a spiral galaxy like the Milky Way from early universe'' (December 3, 2025)- A report on how Indian researchers discovered a massive galaxy that existed when the universe was just 1.5 billion years old , one of the earliest to have been observed so far. Signature Beat: Health, Science & Women in Leadership Anuradha is known for her COVID-19 reportage, where she was one of the first journalists to provide detailed insights into the Covishield and Covaxin trials. She has a dedicated interest in gender diversity in health and science, often profiling women researchers who are breaking the "leaky pipeline" in STEM fields. Her writing style is scrupulous, often featuring interviews with top-tier scientists and health experts from various institutions. ... Read More

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