Resilient microbiome and biocultural adaptation: insights from the gut microbiota of India’s particularly vulnerable tribal groups

The human gut microbiome reflects biocultural history but remains largely unexplored in India’s Particularly Vulnerable Tribal Groups (PVTGs), who maintain strong ecological and traditional subsistence relationships. We analysed 234 gut microbiome samples from six communities across three regions of India using shotgun metagenomic sequencing to characterise microbial structure, functional capacity, and microbiome transition status. We have identified three different microbiome clusters across the six communities – SPI ( Spirochete -rich), a well-documented enterotype in global tribal communities, especially the presence of Treponema succinifaciens , SEG ( Segatella -dominated), a common enterotype in Indian communities regardless of geographical region, and FIR ( Firmicutes -enriched), which may be considered “diversified” with nearly no T. succinifaciens , decreased Segatella dominance and increased Firmicutes - Bacteroidetes (FB) ratio. Further, we explored gut microbiome-associated pathways and contributing species responsible for fibre, mucin, complex carbohydrate, dairy substrate degradation, vitamin B, C, and K2 synthesis, SCFA production, Xenobiotic degradation, and LPS and Peptidoglycan synthesis. The variations and similarities observed among the communities signify their lifestyle and dietary practices characterised by the intake of unrefined plant foods, seasonally varied proteins and fibre. Overall, although signs of dietary and microbiome transitions were evident, especially in a few of the samples where FIR-cluster was observed, the increased abundance of Segatella species in SPI and SEG clusters, the presence of T. succinifaciens in these 2 enterotypes, and the presence of fibre degradation pathways in FIR may denote the resilient nature and functional convergence of the gut microbiome in the PVTGs of India. Cataloguing the gut microbiomes of PVTGs at a moment of cultural transition becomes essential for establishing biological and cultural archives. Not applicable.