Altering competition outcomes of a pair of gut bacterial species via manipulation of spatial and temporal structure

The gut microbiome contains hundreds of interacting species that shape host health and disease. To clarify the still poorly understood forces that shape community composition, especially general consequences of spatial and temporal structure, we have made use of larval zebrafish with controlled combinations of intestinal microbes. In earlier work, we discovered a pair of commensal species that exhibits strong competitive interactions. Here, we explore factors that can alter this outcome in favor of either species. A mutant of one of the species, revealed by live in vivo imaging to be less aggregated than the wild type, tunes the competition outcome further in favor of this species. Conversely, the outcome can be shifted in favor of the other species by allowing it to colonize the gut before its competitor. In addition to bacterial dynamics, we observe species-dependent activity of the host immune system, assessed with Tuning two-species competition outcomes could be relevant to manipulating the outcomes of competition in more complex gut bacterial communities.