Microbiome from diverse natural environments colonize and compete in the mouse gut

Mammalian hosts constantly interact with diverse exogenous environmental microbes (such as from soil), but the importance of soil-derived environmental exposure to host health conditions is poorly understood. We here developed a gnotobiotic mouse model that mimics soil-derived microbiota colonization in the early-life gut of mice and subsequent distinct microbial exposure that often occurs when hosts migrated from birthplace to the others. Using metagenomic shotgun sequencing, we first reconstructed colonization patterns of soil microbes from distinct habitats (desert, steppe and forest) in the gut of 90 germ-free mice and competition patterns of those microbiota after a 30-days cross-environmental migrations. Firstly, we found that the early-life microbial exposure established the birthplace-dependent patterns of taxonomic and functional diversity in mice gut microbiome. Secondly, after transferring mice to distinct soil environments, we observed profound and birthplaces-dependent changes in the mice gut microbiome. Moreover, we found that steppe-originate mice have the most active metabolism pathways and are more adaptive to any of new environments thus inferred a existence of certain born condition that is favorable for host development. Remarkably, the birthplace-associated microbial signatures can persist along the study regardless of cross-birthplace emigration and meanwhile will develop corresponding gut microbiome function to adapt certain environments. In summary, our study provided novel insight into the long-lasting effect of environmental-exposure-dependent history on gut microbiome development and underscored the importance of interaction of environment and gut microbiome.