Differential modulation of post-antibiotic colonization resistance to Clostridioides difficile by two probiotic Lactobacillus strains

ABSTRACT Probiotics are often consumed after antibiotic treatment to prevent antibiotic-associated diarrheal disease, most commonly caused by Clostridioides 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 Lactobacillus acidophilus NCFM and Lactobacillus gasseri Lg-36 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 were enriched after L. gasseri administration and associated with colonization resistance. Using Muribaculum intestinale and Duncaniella 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 specific probiotic strains taken after antibiotic treatment and support 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.IMPORTANCEProbiotic research has overwhelmingly generalized the safety of select strains perceived as beneficial, while most studies are based on individual strains to substantiate particular functional attributes. In contrast, Clostridioides difficile studies document how this complex pathogen interacts with diverse members of the gut microbiota to cause diarrheal disease. Despite their purported ability to inhibit pathogens and modulate the gut microbiota, probiotics have been used to treat C. difficile infections with little success. In this study, we examine how common probiotics can impact the recovery of the gut microbiota after antibiotics by measuring colonization resistance against C. difficile in a mouse model. We show that Lactobacillus acidophilus enhances C. difficile infection, while Lactobacillus gasseri promotes colonization resistance potentially through its expression of bacteriocins and an enrichment of Muribaculaceae. This work highlights the complexity of probiotic interactions with pathogens and the indigenous microbiota and further supports that the overlooked Muribaculaceae are capable of inhibiting C. difficile.