A1 Refereed original research article in a scientific journal
Gut microbiomes of tribal communities in India vary with dairy and grain consumption; 
Authors: Ebel, Emily R.; Kulkarni, Abhijit Sanjiv; Mongad, Dattatray S.; Olm, Matthew R.; Devi, Sarangthem Indira; Mir, Bilal Ahmad; Ozarkar, Shantanu; Sonnenburg, Erica D.; Shouche, Yogesh S.; Sonnenburg, Justin L.; Dhotre, Dhiraj P.
Publisher: Informa UK Limited
Publication year: 2026
Journal: Gut Microbes
Article number: 2694242
Volume: 18
Issue: 1
ISSN: 1949-0976
eISSN: 1949-0984
DOI: https://doi.org/10.1080/19490976.2026.2694242
Publication's open availability at the time of reporting: Open Access
Publication channel's open availability : Open Access publication channel
Web address : https://doi.org/10.1080/19490976.2026.2694242
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/527001430
Self-archived copy's licence: CC BY
Self-archived copy's version: Publisher`s PDF
Additional information: Data analysis scripts and tables used in this study are available at https://github.com/emily-ebel/indian-gut-microbiome. Read data and genome assemblies generated by this study are publicly accessible on the short read archive (SRA) and GenBank under NCBI BioProject PRJNA1266865.
Highly diverse gut microbiomes of non-industrialized populations share similarities with ancestral states of symbiosis and are linked to low rates of chronic inflammatory diseases. Yet there is still limited understanding of the diverse array of non-industrialized gut microbiomes throughout the world, including among the tribal populations of India. In this study, we surveyed dietary and fecal microbiome variation among 76 adults from eight tribal communities in four biogeographic regions of India, including Warli on the western coast, Gond and Madia in the northeast Deccan Plateau, Kabui (or Rongmei Naga) in the northeast hills of the Himalayas, and Balti, Boto, Brokpa, and Purigpa in the northwest Trans-Himalayas. Metagenomic and 16S sequencing of fecal samples identified Segatella, Agathobacter, and Faecalibacterium as core members of the gut microbiome of all populations, with Segatella copri (formerly Prevotella copri) dominant at mean 25%–47% relative abundance. Four Trans-Himalayan populations with diets uniquely defined by dairy and diverse cereals had elevated gut alpha diversity and distinct beta diversity, driven by prevalent and abundant Bifidobacterium as well as taxa shared with the ruminant microbiome. Strains of B. adolescentis present in the dairy-consuming populations were genetically distinct from industrialized strains around the world and encoded CAZymes consistent with selection by dairy and grain consumption. The gut microbiomes of a minority of subjects shared taxonomic and functional features with a previously described sample of Californians, suggesting that the pressures posed by globalization could be impacting the microbiomes of tribal populations. These results highlight the nutritional and microbiological contribution of dairy livestock in shaping gut communities and emphasize the large effect that lifestyle can have on the diversity and function of non-industrialized gut microbiomes.
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Funding information in the publication:
This work was supported by the Department of Biotechnology (DBT, India) BRIC-National Center for Cell Science (NCCS) to DD. DD is Principal Investigator at BRIC-National Center for Cell Science (NCCS). ASK was supported by the Department of Biotechnology (DBT, India) with PhD fellowship grants to conduct this study. This work was supported by National Institutes of Health (United States) grants DP1-AT009892 and R01-DK085025 to JLS and by Open Philanthropy. JLS is a Chan Zuckerberg Biohub Investigator, and metagenomic sequencing in this study was made possible by the Chan Zuckerberg Biohub. ERE was supported by a National Science Foundation (United States) Postdoctoral Research Fellowship in Biology (#2109851). The funders played no role in the study design, data collection, data analysis, decision to publish, or preparation of the manuscript. The content of this work is solely the responsibility of the authors and does not necessarily represent the official views of the funders, governments, or academic institutions.
