From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia

Despite established roles in human health and profound global diversity, existing gut microbiome datasets are biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a novel gut microbiome dataset from 116 Indonesian individuals representing a diverse cline from transitional hunter-gatherers to rural agricultural to urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species (15%) and subspecies-level (50%) novelty. Novel taxa are rare, often village-specific, and depleted for sporulation genes, revealing a direct link between bacterial physiology, transmission, prevalence and discovery. We reveal reduced microbial diversity associated with rural-to-urban transition, and also multi-layered patterns across taxonomic levels, including opposing trends within genera. Furthermore, community membership, over diet, is often a stronger predictor of microbiome composition. Our work highlights the interplay of host behaviour, population structure and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities