What Moving to a City Does to the Gut Microbiome, Across Ten Communities

There is a tidy story about cities and digestion that has been told for about a decade now: people move to town, the diet narrows, the microbiome thins out, and everyone ends up with the same depleted gut. It is a good story. A survey of 575 people across ten communities in India and Sri Lanka suggests it is also too simple.

The studyWhat is the SAMBAR cohort?

SAMBAR — the South Asian MicroBiome ARray — is a population-scale study of 575 adults from ten communities across India and Sri Lanka, sampling rural and urban participants from each. It is among the most culturally diverse surveys of the South Asian gut microbiome to date.

Published in Gut Microbes in July 2026, the work was led from the University of Chicago with collaborators in India, Sri Lanka and the United States. The communities span an unusual range: Spitians from the Indian Himalayas; Gond, Kolam and Koya from central India; Kani from the south; Mizo and Pochury Naga from the northeast; and Adivasi, urban Sinhalese and urban Tamil communities in Sri Lanka.

The headline resultDoes urbanisation change the gut microbiome the same way everywhere?

No. The researchers found that urbanisation affected every community studied, but the size and character of the change differed markedly between them. There was no single shared trajectory into a common urban microbiome.

This is the finding worth sitting with, because it cuts against the received version. As the team put it, “different communities have unique microbial signatures that reflect their cultures and diets and respond to urbanization in different ways.” The University of Chicago account is blunter still about the ranking: geography and community affiliation explained more of the variation in gut microbiome composition than whether a person lived rurally or in a city.

The specificsWhich bacteria varied between communities?

Three came up by name. Bifidobacterium tracked with wheat and yogurt consumption and varied by community. Megamonas, linked to fat metabolism, rose in urban groups across several communities. Bacillus was markedly higher among Pochury participants who eat axone, a fermented soybean condiment.

The axone result is a useful illustration of why the averaging approach fails. A single regional ferment — not a national diet, not an income bracket, not a rural-versus-urban category — produced one of the clearest microbial signals in the dataset. Any study design that pooled these communities into a single South Asian group would have flattened that away entirely.

Urban cohorts did generally show lower microbial diversity than rural ones, which is consistent with what has been reported elsewhere. But it sat alongside community-specific patterns large enough that the researchers declined to describe urbanisation as one process.

The wider pointWhy does it matter that the study was done in South Asia?

Most large microbiome datasets come from a narrow slice of the world. The researchers found South Asian communities occupied a distinct position within global gut microbiome diversity, arguing that reference data drawn mainly from Europe and North America is incomplete.

The consequence is practical rather than abstract. When a laboratory or a consumer test describes a microbiome as normal, unusual, or depleted, it is comparing against a reference population. If that reference is built mostly from one part of the world, then normal is a local measurement wearing a universal label. A study like this one widens the frame it is measured against.

The limitsWhat does the study not tell us?

It describes composition at a point in time, not health outcomes. It did not follow individuals as they moved, did not test whether any of the differences affect wellbeing, and does not indicate that one community’s microbiome is better than another’s.

Lower diversity in urban cohorts is frequently reported as though diversity were a score to be maximised. The relationship is not that clean, and this study does not make it so — it measured who was there, not what it did. Nor does the work say anything about what any individual reader should eat, which is a question it was never built to answer.

What it does offer is a correction to a habit of mind. The gut microbiome has often been discussed as though there were one healthy destination and a set of universal routes toward it. Ten communities across two countries, each arriving somewhere different, is an argument that the map is larger than the version most of us have been shown.