Differences in Gut Microbiota Assembly Alter Its Ability to Metabolize Dietary Polysaccharides and Resist Clostridioides difficile Colonization

The mammalian gut is home to a vibrant community of microbes. As the gut microbiota has evolved, its members have formed a complex yet stable relationships that prevent non-indigenous microorganisms, such as Clostridioides difficile, from establishing within the gut. Using a bioreactor model of the gut, we characterize how variation in microbial community assembly changes its ability to resist C. difficile. We established diluted microbial communities from healthy human stool in a bioreactor gut model and subsequently challenged them with vegetative C. difficile. 16S rRNA-gene sequencing and selective plating revealed that dilution progressively increases microbiota variability and decreases C. difficile colonization resistance. Using Dirichlet Multinomial Mixtures and linear discriminant analysis of effect size, we identified 19 bacterial taxa, including Bifidobacterium, Bacteroides and Lachnospiraceae, that associate with more resistant community types. Since these taxa are associated with butyrate production, which is tied to C. difficile colonization resistance, we performed another reactor experiment where we increased inulin concentrations prior to C. difficile challenge. Diluted communities concurrently lost their ability to produce additional butyrate in response to inulin, as measured by high performance liquid chromatography, and resist C. difficile colonization. These data demonstrate that a similar level of microbiota cohesiveness is required to prevent C. difficile colonization and metabolize inulin. It also suggests that metabolic activity of butyrate-producing microbes is tied to colonization resistance. Future work can leverage these findings to develop treatments that leverage knowledge of these ecological dynamics to improve efficacy. ImportanceThe microbes living in the human large intestine helps create an environment that is resistant to organisms that do not normally reside there, such as the pathogen Clostridioides difficile. Differences in ways in which microbial communities make an environment their home can change their ability to provide that resistance. To study those differences, we use a model of the intestine that incorporates only microbial variables (i.e. no host is involved). By diluting microbial communities to decrease their complexity, we show that communities lose their ability to resist C. difficile at a particular point and, at the same time, their ability to use inulin, a common dietary fiber, in ways that make the environment more toxic to C. difficile. These findings will help future researchers dissect the microbial components that create a resistant intestinal environment.