Species covariance in <i>C.</i> e<i>legans </i>microbiome demonstrates existence of bacteria-bacteria and host-bacteria interactions

The structure and internal dynamics of complex microbial communities in the guts of organisms is poorly understood. Here we analyze a simplified community of bacteria in the gut of Caenorhabditis elegans, a roundworm. Initially germ-free adult C. elegans are introduced into an environment with equal concentrations of eight bacterial species from a native worm microbiome. After four days, we examine individual worm gut communities and calculate the covariance structure of the bacterial abundances. 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 birth 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.