Microbial dispersion in the human gut through the lens of fecal transplant

Abstract

Microorganisms frequently migrate from one ecosystem to another, influencing and shaping their new environment. Yet, despite the potential importance of this process in modulating the environment and the microbial ecosystem, our understanding of the fundamental forces that govern microbial migration and dispersion is still lacking. Moreover, while theoretical studies and in-vitro experimental work have highlighted the contribution of biotic interactions to the assembly of the community, identifying such interactions in vivo, specifically in communities as complex as the human gut, remains challenging. To this end, we developed a new, robust, and compositionally invariant approach, and leveraged data from well-characterized translocation experiments, namely, clinical fecal microbiota transplant (FMT) trials, to rigorously pinpoint dependencies between taxa during the colonization of human gastrointestinal habitat. Our analysis identified numerous pairwise dependencies between co-colonizing microbes during migration between gastrointestinal environments. We further demonstrated that identified dependencies agree with previously reported findings from in-vitro experiments and population-wide distribution patterns. Finally, we characterized the web of metabolic dependencies between these taxa and explored the functional properties that may promote better dispersion. Combined, our findings provide insights into the principles and determinants of community dynamics following ecological translocation, informing potential opportunities for precise community design.