The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods, and appear to assemble in a predictable manner. This stability is considered critical for good health but is poorly understood. Here we develop a body of ecological theory to help us understand microbiome stability and initial assembly.
Although cooperating networks of microbes can be efficient, we find that they are often unstable and challenging to assemble. Counterintuitively, this finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability. More generally, stability is promoted by limiting positive feedbacks and weakening ecological interactions. In the light of this, we analyze host mechanisms for maintaining stability, including immune suppression, spatial structuring, and feeding of community members, and discuss our key predictions in the context of recent data.