Quantifying multi-species bacterial interactions in larval zebrafish

The microbial communities resident in animal intestines are composed of many species and play an important role in host development, health and disease. The complex nature of these diverse communities makes it challenging to determine the driving forces behind microbial composition. Further, it is unclear for many multi-species consortia whether species-level makeup can be predicted based solely on pairwise inter-species interactions, or whether higher-order interactions are needed to explain the composition of these 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 dissection and plating assays we demonstrate the construction of communities of 1 to 5 bacterial species and show that the outcomes from the 2-species competitions do not contain enough information to predict the abundances in more complex communities. Furthermore, we observe a dampening of strong negative interactions as the microbial composition of the gut becomes more diverse. Our data suggests higher order interactions are important in the zebrafish gut, possibly due to changes in spatial organization that ongoing live imaging experiments are illuminating.