Distinct trajectories of urbanization shape the human gut microbiome across South Asia

Ramachandran, S. L.; Pasupuleti, N.; Abdill, R. J.; Adikari, G.; Ahlawat, B.; Blekhman, R.; Burgo, V.; Davenport, E. R.; Dwivedi, A.; Gupta, S.; Ijinu, T. P.; Jamir, T.; Karu, R.; Kaushik, A.; Komarabathini, J. M.; Laithangpuii,; Lalzarliana, J.; Norbu, T.; Pautu, T.; Pawar, K.; Raman, A. S.; Ramaswamy, R.; Ranasinghe, R.; Rashmi,; Sasidharan, S. P.; Satheesh, T.; Shaji, S.; Shapiro, J. W.; Singh, E.; Singson, V.; Sundararajan, A.; Tennekoon, K. H.; Tetso, D.; Urban Aragon, J. A.; Welikala, A. H. J.; Yhome, R. R.; Rai, N.; Raghavan, M.

doi:10.64898/2026.01.22.701183

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bioRxiv · 10.64898/2026.01.22.701183

Distinct trajectories of urbanization shape the human gut microbiome across South Asia

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Abstract

Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Although urbanization is consistently associated with increased abundance of disease-linked taxa, microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat- and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase non-persistence. Microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography and underscoring the need for community-specific investigations of health impacts.

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Ramachandran, S. L., Pasupuleti, N., Abdill, R. J., Adikari, G., Ahlawat, B., Blekhman, R., Burgo, V., Davenport, E. R., Dwivedi, A., Gupta, S., Ijinu, T. P., Jamir, T., Karu, R., Kaushik, A., Komarabathini, J. M., Laithangpuii,, Lalzarliana, J., Norbu, T., Pautu, T., Pawar, K., Raman, A. S., Ramaswamy, R., Ranasinghe, R., Rashmi,, Sasidharan, S. P., Satheesh, T., Shaji, S., Shapiro, J. W., Singh, E., Singson, V., Sundararajan, A., Tennekoon, K. H., Tetso, D., Urban Aragon, J. A., Welikala, A. H. J., Yhome, R. R., Rai, N., Raghavan, M.. 2026-01-23. Distinct trajectories of urbanization shape the human gut microbiome across South Asia. https://doi.org/10.64898/2026.01.22.701183

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