Interspecies Bacterial Competitive Outcomes in C. elegans Intestine Reveal the Principles of Community Assembly in a Simple Animal Gut

Animals throughout the tree of life contain complex multi-species gut communities that play an important role in health and disease. However, the complexity of these gut microbiomes often constrains our ability to gain a mechanistic understanding of how these communities assemble and function. We colonize the gut of the worm C. elegans, a tractable experimental system, with 11 bacterial species in singles, all possible pairs, and selected trios. We find a mixture of coexistence and competitive exclusion with a hierarchical structure lacking any rock-paper-scissors interactions. With the intention of associating the characteristics of these one, two, and three species microbiomes, we find a correlation between the monoculture colonization capacity of a bacteria and its average fraction at pairwise competition, and we encounter that the fractions of pairwise competitions possess good predictive power of trio outcomes. We further show that the C. elegans gut environment changes the outcome a pair of species would have outside of the host, with the low intestinal pH being one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and function of complex microbial communities.