Pairwise and Multi-Species Interactions Among Larval Zebrafish Gut Microbiota

The microbial communities resident in animal intestines play important roles in health and disease, and are composed of dozens to hundreds of interacting species. The determinants of this composition, which may include physical characteristics of bacterial groups as well as biochemical interactions between species, remain largely unknown. More generally, it is unclear for many multi-species consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions, or whether higher-order interactions are necessary to explain community assembly.

To address this, we consider commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. Using a combination of conventional dissection and plating assays and three-dimensional live imaging, we demonstrate the existence of stable multi-species communities and test whether outcomes from two-species competitions contain enough information to allow prediction of multi-species abundances and interactions. We also compare in vitro competitions of the same commensal species, in which the spatial, temporal and nutritional heterogeneity of the intestine is absent.