Gut-microbe study races to capture what urban diets erase in urbanising India

Bacteria in the human gut, and not just genes, may help explain why urbanising Indians face rising rates of diabetes, obesity and hypertension. This is from a three-year study that has produced what its authors describe as the first reference database of the gut microbiome across South Asia.

The study, published in the peer-reviewed Gut Microbes, sampled 575 adults from 10 communities across India and Sri Lanka and profiled their gut bacteria through gene. Niraj Rai of the Birbal Sahni Institute of Palaeosciences, Lucknow, who led the work with Maanasa Raghavan of the University of Chicago, said India offered a rare natural experiment. “India is the only country where you can still find a rural versus urban” population that shares ancestry but lives in very different food environments, he said.

India has an estimated 89.8 million adults living with diabetes as of 2024, according to the International Diabetes Federation’s latest. This is the second-largest burden in the world after China, and roughly one in every seven adults with the disease globally. The federation projects India’s total will climb about 75% to reach 156.7 million by 2050, even as an estimated 43% of cases currently go undiagnosed. Worldwide, 589 million adults are estimated to have diabetes. The disease’s steep rise in India has been driven in large part by rapid urbanisation and dietary change — the very transition this study set out to read in the gut.

The researchers designed their study by pairing each remote, forest-dwelling or early-agriculturalist community with relatives who had migrated to towns and cities with access to processed food — “pizza, chowmein, coke,” in Mr. Rai’s description. Because both groups share genetic ancestry, verified by genome sequencing, Mr. Rai argued that differences in their microbiomes must stem from environment rather than genes. Sri Lanka’s Vedda, among the region’s oldest hunter-gatherer settlers, were included because they remain genetically South Asian while retaining a foraging lifestyle that Mr. Rai said approximates an “ancient gut signature.”

The clearest example of environment reshaping the same genetics is Megamonas, a bacterium the study found consistently more abundant in urban individuals than in their rural kin. Megamonas has been linked worldwide to obesity, hypertension and raised blood glucose; the paper reports a significant association with blood glucose and a known mechanism involving lipid absorption. “We are reporting for the first time that Megamonas are thriving because of a change in diet,” Mr. Rai said. 

Running the other way is Holdemanella, associated with fibre intake and glucose tolerance, prevalent in South Asia but apparently lost with urbanisation — except in Kerala, Mr. Rai noted, where communities largely kept traditional diets even after migrating.

Mr. Rai framed urbanisation as a matter of food processing rather than meat-eating. In the northeast, he said, rural and urban communities both eat meat; the urban difference is the biscuit, the soft drink, the occasional pizza.

The findings also push against a long-standing account of dairy in the subcontinent. The lactase-persistence gene, which lets adults digest milk, is usually traced to migrations from the northwest and ultimately Anatolia and the steppe around 4,000 to 5,000 years ago. But Mr. Rai pointed to pastoral communities — Ladakhis, the Toda and Kota, the Kadu Golla — who he said consumed milk far earlier, and whose guts carry bacterial signatures capable of breaking down lactose. Screening more than 10,000 samples, the team found little correlation with lactase-persistence genotypes, Mr. Rai said, suggesting the mutation was “an additional benefit” rather than a requirement, with the responsible bacteria positively selected at the community level over a long period.

Microbiome research matters, Mr. Rai said, because gut bacteria act as an environmental factor that modifies how genes are expressed — comparable to the way smoking amplifies inherited cancer risk. A person carries up to a kilogram of gut bacteria, partly inherited from their parents, and altering it may eventually become a route to therapy, he reckoned.

The project is now moving to a functional phase. Mr. Rai’s team has begun metabolomics — profiling the molecules these bacteria produce — to connect specific microbes to specific diseases. By year’s end, he expects roughly 1,000 samples, including from the Andaman and Nicobar Islands, where the team has secured approval to sample isolated communities this winter. Mr.Rai believes the window is closing. “No one can do such a study,” he said, “because everywhere now the roads are coming.