Interactions and structure of native gut microbiome ofC. elegans

Microbial communities are finite non-equilibrium systems, where the underlying interaction networks play out under environmental perturbation and drift due to migration and demographic stochasticity. The interactions among microbes (direct) and between microbes and the host (indirect) form a network, and efforts have been devoted to extracting these networks of interactions from co-occurrence data. However, how these interactions between microbes collectively form a microbiome is still not completely known. Here, eight bacterial species from a native C. elegans microbiome were cultivated in vitro and used to colonize sterile nematode gut. From in vitro data, we observed a range of inter-species interactions, and colonizing the gut with individual species revealed intestinal populations that increase over time, consistent with a simple Lotka-Volterra-type model for saturating growth. These bacterial populations are apparently multimodal across populations of homozygous, synchronized hosts. Using the experimental data to fit a simple mathematical model, we aim to understand the contribution of direct vs. indirect interactions in minimal native microbiome assembly, considering the contributions of noise and of heterogeneity across individual hosts.