Environmental, Socioeconomic, and Health Factors Associated with Gut Microbiome Species and Strains in Isolated Honduras Villages

Abstract

ABSTRACTDespite a growing interest in the gut microbiome of non-industrialized countries, data linking microbiome features from such settings to diverse phenotypes remains uncommon. Using metagenomic data from a community-based cohort of 1,871 people from isolated villages in the Mesoamerican highlands of western Honduras, we report novel associations between bacterial species and phenotypes. We also find an uncharacterizedLachnospiraceaespecies associated with 22 different phenotypes, and little overlap with a prior Dutch Microbiome Project. Furthermore, including strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially in some phenotypes like household wealth. Coincidentally, wealthier individuals also have a higher number of polymorphic sites. Our analysis suggests new roles that gut microbiome surveillance can play in understanding broad features of individual and public health.