16S Sequencing of murine fecal and cecal samples

Probiotics are often consumed after antibiotic treatment to prevent antibiotic-associated diarrheal disease, most commonly caused by C. difficile. However, the impact of probiotic bacteria on the post-antibiotic gut microbiota is undetermined and often overlooked. Here, we examined the effect of a single dose of probiotic L. acidophilus and L. gasseri on colonization resistance against C. difficile in an antibiotic-treated mouse model. We found that L. acidophilus administration increased C. difficile infection and impaired the restoration of colonization resistance. In contrast, L. gasseri decreased C. difficile and promoted the return of colonization resistance, presumably through a putative bacteriocin inhibiting C. difficile. However, L. gasseri transiently colonizes the mouse gut and its administration impacts colonization resistance after it is no longer detectable. We analyzed the gut microbiota of mice and found that members of the understudied Muribaculaceae family are enriched after L. gasseri administration and are associated with colonization resistance. Using M. intestinale and D. muris, we determined that elevated growth of these species can restrict C. difficile growth in vitro, suggesting that these bacteria may play a role in establishing colonization resistance in vivo. These findings highlight the potential pitfalls of probiotics taken after antibiotic treatment and supports the need for further investigations of their influence on the gut microbiota post antibiotic. Additionally, this work supports the role of the Muribaculaceae as beneficial gut commensals that can contribute to colonization resistance against C. difficile, and illustrates the need to decipher community interactions in complex microbial consortia.