Live imaging reveals connections between aggregation and competition among a pair of gut bacterial species

The gut microbiome contains hundreds of interacting species that shape host health and development. Despite their significance, the driving forces of community composition remain poorly understood. We focus on the role of physical factors such as spatial structure on inter-species competition, examining a pair of bacterial species native to the zebrafish gut, namely Aeromonas (AE) and Enterobacter (EN), that both form dense aggregates with similar spatial distributions in the intestine. If co-inoculated, EN faces stiff competition that can be tuned in its favor by allowing it to colonize first. A mutant of AE (AE-MB4), revealed by live imaging to consist mostly of planktonic cells rather than aggregates, has a different spatial distribution than the wild type. Despite the reduction in spatial overlap, EN fares even worse in competition with AE-MB4, even when EN is established first. Strikingly, AE-MB4 induces rapid fragmentation of EN aggregates into planktonic individuals with a low growth rate. In the presence of other commensal bacterial species, we observe a dampening of the strong competition, a rescue of the abundance and spatial distribution of EN and aggregation of AE-MB4, suggesting multi-species communities promote co-existence in the larval zebrafish gut.