Examining Pairwise and Multi-Species Interactions in Larval Zebrafish

The microbial communities resident in animal intestines are composed of dozens to hundreds of species and play important roles in host health and disease. The determinants of microbial composition, which may include physical characteristics or biochemical interactions, remain largely unknown. Further, 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 needed to explain community assembly. It is also unclear how spatial organization plays a role in determining the make up of these complex communities.
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 dissection and plating assays and 3-dimensional live imaging, we demonstrate the construction of communities of 1 to 5 species and test whether outcomes from 2-species competitions contain enough information to predict the abundances in more complex communities. We also quantify changes in species’ spatial distributions induced by the presence of other species, which may explain correlations in their abundances.