Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

To study how microbes establish themselves in a mammalian gut environment, we colonized germ-free mice with microbial communities from human, zebrafish, and termite guts, human skin and tongue, soil, and estuarine microbial mats. Bacteria from these foreign environments colonized and persisted in the mouse gut; their capacity to metabolize dietary and host carbohydrates and bile acids correlated with colonization success. Cohousing mice harboring these xenomicrobiota or a mouse cecal microbiota, along with germ-free “bystanders,” revealed the success of particular bacterial taxa in invading guts with established communities and empty gut habitats. Unanticipated patterns of ecological succession were observed; for example, a soil-derived bacterium dominated even in the presence of bacteria from other gut communities (zebrafish and termite), and human-derived bacteria colonized germ-free bystander mice before mouse-derived organisms. This approach can be generalized to address a variety of mechanistic questions about succession, including succession in the context of microbiota-directed therapeutics. [Display omitted] •Microbiota from diverse habitats colonize and compete in the guts of gnotobiotic mice•Ecological succession cannot be predicted solely from microbes’ typical habitats•Opportunist microbes can be identified and displaced by better host-adapted microbes•The approach can address mechanistic questions relevant for microbiota therapeutics Cohousing mice colonized with different microbial sources reveal competitive dynamics among species and establish a system to probe how established microbiota permit or resist colonization by microbes from other communities.