Animals harbor gut microbiotas that play critical roles in the maintenance of host health, from digestion to immunity. Characterizing the gut microbiota has become an active area of research, but the relative contribution of factors shaping microbiota composition is still unclear. C. elegans could provide a useful model to study such questions, utilizing genetically homogenous populations to discern common patterns in microbiota composition beyond individual variation. However, to date, very little is known about the natural C. elegans microbiota. To fill this gap, we grew worms of the N2 wildtype strain in the lab in natural-like mini-environments of different composted soils, and used 16S rDNA deep sequencing to characterize the assembled microbiota of adult worms. Comparisons of worm microbiotas to microbiotas in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments. This enabled defining a core gut microbiota that accounted for ca. 50% of gut microbes, and was primarily composed of members of the Enterobacteriaceae, Pseudomonadaceae, and Xanthomonadaceae families. Beyond the shared core, two distinct types of worm microbiotas were identified, distinguished by varying abundance of core taxa as well as the presence of auxiliary taxa. Ecological analyses indicated that the assembly rules for worm microbiotas differed from those in their soil habitat, and pointed at the importance of competitive interactions between gut-residing taxa. Our results support a dominant contribution of the host niche in shaping the gut microbiota, and suggest contributions from inter-microbial competition within the gut. The data presented provides a framework to better understand the worm natural history and its interactions with microbes.
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