Stochastic Assembly Produces Heterogeneous Communities in the C. elegans Intestine

Host-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this heterogeneity. Here we demonstrate that stochastic bacterial community assembly in the C. elegans intestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities. Introduction The gut microbiome varies greatly between individuals, and this variation could have important health consequences (1,2). These differences may be due to genetic differences between individuals, to differences in individual history and environmental exposure, and to stochasticity (3,4), but the relative contributions of these factors are difficult to determine. Extensive research has focused on the deterministic factors directing microbial community composition (5–7). Indeed, the canonical understanding of community assembly is based on deterministic niche-based processes, which push communities toward equilibria determined by the species present and the resources available. Under this view, if individual hosts are exposed to similar species and contain similar environmental conditions, they are expected to converge to similar community compositions. By contrast, where stochastic processes dominate, similar hosts exposed to identical environmental conditions can diverge considerably in their final community composition. This will be the case where migratory and other