Urbanization is one of the most consequential demographic shifts of the 21st century. As communities move from traditional or rural to urbanized ways of life, changes in diet, lifestyle, and environmental exposures can influence many aspects of human biology and health. Research has shown that urbanization can alter the gut microbiome, the community of microorganisms inhabiting the digestive tract, but whether this transition follows a common pattern across different global populations has remained unclear.
South Asia is uniquely suited to address this question because it combines extraordinary cultural, dietary, and ecological diversity with some of the world's fastest rates of urbanization. As lifestyles change, the region is also experiencing a rapid rise in cardiometabolic disorders, such as type 2 diabetes, heart disease, and obesity, making it increasingly important to understand how urbanization shapes the gut microbiome. Despite this, South Asian populations remain underrepresented in global microbiome research.
A new study published in Gut Microbes addresses this gap through one of the most geographically and culturally diverse surveys of the South Asian gut microbiome to date. An international team of researchers from India, the United States, and Sri Lanka reports findings from the South Asian MicroBiome ARray (SAMBAR), a population-scale cohort of 575 adults from ten communities across India and Sri Lanka: Spitians from the Indian Himalayas; Gond, Kolam, and Koya from Central India; Kani from South India; Mizo and Pochury Naga from Northeast India; and Adivasi alongside urban Sinhalese and urban Sri Lankan Tamil communities from Sri Lanka.
By recruiting rural and urban participants across these communities, the researchers were able to investigate whether gut microbiome changes accompanying urbanization follow similar or distinct trajectories across South Asia and how these trajectories, in turn, compare with urbanization-related gut microbiome shifts reported elsewhere in the world.
The study adopted a community-engaged approach throughout the research process. "Establishing SAMBAR required extensive fieldwork across India and Sri Lanka, bringing together researchers, local collaborators, and participating communities spanning ten geographically and culturally distinct populations," said Nagarjuna Pasupuleti, PhD, one of the first authors of the study who led field operations and data generation. "These collaborations were fundamental not only to making this study possible, but also to ensuring that study findings were returned to participating communities through accessible presentations and discussions."
Influence of local diets, environments, and culture
The researchers found that geography and community affiliation explained more of the variation in gut microbiome composition than rural or urban lifestyle alone. Although urbanization consistently influenced the gut microbiome, the magnitude and nature of these changes differed among communities, reflecting differences in local diets, environments, and cultural practices.
"By studying rural and urban participants from multiple communities, we could ask not only whether urbanization changes the gut microbiome, but whether that transition unfolds similarly across populations," said Shreya Ramachandran, PhD, postdoctoral researcher at the University of Chicago and one of the first authors of the study who led the data analyses. "We learned that South Asian communities are heterogeneous, and different communities have unique microbial signatures that reflect their cultures and diets and respond to urbanization in different ways."
The study identified associations between gut bacteria and dietary patterns. For instance, bacteria such as Bifidobacterium were associated with wheat and yogurt consumption. In some communities, this genus was abundant in both rural and urban cohorts, reflecting a tradition of pastoralism and dairy consumption; in some, it was significantly more present in the urban cohorts, reflecting the increase in consumption in cities.
The diverse study population also allowed researchers to identify culturally specific links between diet and bacteria, including a significantly higher abundance of the genus Bacillus among Pochury participants, who regularly consume a Bacillus-heavy fermented soybean condiment called axone.
After accounting for the cultural heterogeneity, the study design allowed the researchers to identify broad patterns of microbial shifts associated with urbanization. For instance, multiple communities showed decreased diversity and an increase in Megamonas in urban cohorts – a genus associated with fat metabolism and with metabolic outcomes including obesity.
Expanding microbiome research globally
The researchers also compared the SAMBAR data with previously published microbiome datasets from other world regions. South Asian communities occupied a distinct position within global gut microbiome diversity, reinforcing the importance of expanding microbiome research beyond populations that have historically dominated biomedical studies.
"South Asia is undergoing rapid and heterogeneous urbanization alongside a growing burden of cardiometabolic disease. Understanding how the gut microbiome changes during these transitions will be essential for interpreting future links between lifestyle, metabolism, and health across the region," said Niraj Rai, PhD, group leader at the Birbal Sahni Institute of Palaeosciences and one of the senior authors.
"As microbiome-based diagnostics and therapies continue to develop, they must be informed by data that reflect the diversity of human populations and the different pathways through which lifestyles are changing," said Maanasa Raghavan, PhD, Assistant Professor of Human Genetics at the University of Chicago and one of the senior authors. "Resources like SAMBAR help broaden that perspective by bringing historically underrepresented populations into global microbiome research."
The authors hope that SAMBAR will serve as a foundational resource for future studies investigating how changing diets, environments, and lifestyles influence the gut microbiome and health across South Asia, while providing a framework for microbiome studies in other underrepresented populations.
