Host heterogeneity in C. elegans drives variation in gut microbial composition

Microbiomes are coexisting communities of microbes that are important for the functioning and health of the host. Microbiome composition and structure vary across individual hosts, but the sources of variation observed in microbiomes are not understood. Differences in interactions among microbes and between microbes and the host can contribute to this variation. We use a bottom-up experimental approach to understand microbiome assembly rules from in vivo monocolonization of the C. elegans gut by members of the native worm microbiome. We measure variation in bacterial abundance across the population of clonal hosts at different times in the colonization process. By fitting the resulting data to a simple stochastic model, we extract parameters of host-microbe association and identify sources of inter-host variation. To the extent that large inter-host variation is present even when bacterial interactions are eliminated, host heterogeneity drives the colonization variability. These results provide an initial step in understanding the role of host heterogeneity in general assembly rules for C. elegans gut microbiome.