Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut

Gastrointestinal colonization by commensal bacteria is a reproducible yet complex process. Mapping the spatiotemporal and genetic factors driving microbial colonization of the gut is key to understanding the gut microbiome and improving clinical interventions that treat dysbiosis. Here, we explored a murine gut colonization model that leveraged the natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of fecal microbiota transplantation (FMT). We identified a natural super-donor consortium that universally engrafts into diverse recipients and resists reciprocal colonization. Upon FMT, the super-donor microbiota displaces a significant fraction of the recipient microbiome and stably persists over months. Metagenomic sequencing of this consortium revealed diverse metabolic genes that could participate in nutrient niche expansion. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 hours followed by a slower emergence of late colonizers over 15-30 days. Moreover, microbial engraftment was localized to specific compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization and functional studies suggested that stable engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia, many of which belonged to the Bacteroidales order. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally-mediated manner to promote successful engraftment into a resident gut microbiome. ### Competing Interest Statement The authors have declared no competing interest.