Bacterial species abundance covariance structure in <i>C. elegans</i> shows signatures of bacteria-bacteria and host-bacteria interactions

The internal dynamics and assembly of microbial communities in the guts of organisms is poorly understood. We analyze a simplified microbiome in the gut of Caenorhabditis elegans, a roundworm. Germ-free adult C. elegans are placed in an environment with equal concentrations of eight bacterial species from the native worm microbiome. After four days, we determine abundances of these bacterial species within individual worm gut communities and calculate their covariance structure. We find statistically significant off diagonal covariances. We demonstrate that a simple model only considering migration, birth, death, and competition for space among the bacteria can capture the mean values of bacterial abundances and their variances. However, it is incapable of explaining the off-diagonal covariances. We also show that the positive off diagonal covariances can be partially explained by variation of the death rate and other bacterial parameters among the worm hosts. However, to explain the off diagonal negative covariances observed in the experiment requires interactions between bacteria beyond competition for space. We thus show that the structure of the microbiome is affected by both bacteria-bacteria and bacteria-host interactions.