The initial gut microbiota and response to antibiotic perturbation influence Clostridioides difficile colonization in mice

The gut microbiota has a key role in determining susceptibility to Clostridioides difficile infections (CDIs). However, much of the mechanistic work examining CDIs in mouse models use animals obtained from a single source. We treated mice from 6 sources (2 University of Michigan colonies and 4 commercial vendors) with clindamycin, followed by a C. difficile challenge and then measured C. difficile colonization levels throughout the infection. The microbiota were profiled via 16S rRNA gene sequencing to examine the variation across sources and alterations due to clindamycin treatment and C. difficile challenge. While all mice were colonized 1-day post-infection, variation emerged from days 3-7 post-infection with animals from some sources colonized with C. difficile for longer and at higher levels. We identified bacteria that varied in relative abundance across sources and throughout the experiment. Some bacteria were consistently impacted by clindamycin treatment in all sources of mice including Lachnospiraceae, Ruminococcaceae, and Enterobacteriaceae. To identify bacteria that were most important to colonization regardless of the source, we created logistic regression models that successfully classified mice based on whether they cleared C. difficile by 7 days post-infection using community composition data at baseline, post-clindamycin, and 1-day post-infection. With these models, we identified 4 bacteria that were predictive of whether C. difficile cleared. They varied across sources (Bacteroides), were altered by clindamycin (Porphyromonadaceae), or both (Enterobacteriaceae and Enterococcus). Allowing for microbiota variation across sources better emulates human inter-individual variation and can help identify bacterial drivers of phenotypic variation in the context of CDIs.