Abstract
A detailed understanding of human gut microbial ecology is essential to engineer effective microbial therapeutics and to model microbial community assembly in health and disease. However, establishing generalizable insights into the functional determinants of microbial fitness in the gut has been a formidable challenge. Here we employ fecal microbiota transplantation (FMT) as an in natura experimental model to identify determinants of microbial colonization and resilience. Our findings reveal adaptive ecological processes that favor high-fitness populations with higher metabolic competence as the main driver of microbial colonization outcomes after FMT. We further show that while healthy individuals harbor both low-fitness and high-fitness populations, individuals with inflammatory bowel disease are typically depleted of low-fitness populations. These results offer a model to explain why common yet typically rare members of healthy guts can dominate under inflammatory conditions without any need for them to be causally associated with, or contribute to, such disease states.
Competing Interest Statement
The authors have declared no competing interest.
