Lifestyle transition from rural to urban setting changes the gut bacterial profile in an ethnic community of northeast India

The human gut microbiome undergoes transformation due to various exogenous and endogenous influences. Lifestyle has been one of the major contributors of gut microbiome composition. Our study investigated the effect of migration on the gut microbiome of the Mishing ethnic community in India associated with urban migration from their pastural lifestyle. Gut bacterial diversity was profiled using 16S rRNA amplicon sequencing. We observed notable alterations in microbial diversity and composition, including changes in the core microbiome. While Bifidobacterium, Lactococcus and Streptococcus significantly increased (p < 0.01) among the migrant population there was depletion in bacteria such as Succinivibrio and Prevotella. This change in core microbiome was further reflected on the functional profile of the bacterial community harbored by the urban and rural dwellers. While the rural population was enriched in fatty acid biosynthesis pathways, amino acid and Vitamin B2 biosynthesis pathways were more prominent in the microbiome of the urban dwellers. We further observed increase in diversity and richness of the microbiome following migration. Co-analysis with ASVs from food samples consumed by the Mishing rural population revealed that 51 ASVs among the rural dwellers were from a widely consumed beverage, Apong which were completely absent among the migrants. Our analyses highlight the dietary preferences, particularly abstinence from specific foods and beverages, may modulate the alterations in gut microbial profiles. While the cross-sectional design and amplicon sequencing limited our ability to assess temporal and functional changes, our findings highlight a measurable impact of lifestyle and dietary transitions on the gut microbiome.