Adjunct probiotic therapy has the potential to decrease Clostridium difficile disease incidence and severity. After screening several potential probiotic bacteria for intrinsic resistance to C. difficile antibiotics (vancomycin, metronidazole and fidaxomicin), we determined that L. reuteri strains are ideal adjunct therapy candidates. We evaluated the ability of reuterin - a secondary metabolite produced by specific strains of L. reuteri during fermentation of the prodrug glycerol - to inhibit C. difficile growth in vitro. We found that levels of reuterin produced by L. reuteri 17938 were more potent than vancomycin in inhibiting C. difficile growth. Using human fecal microbiota bioreactors, we showed that co-delivery of L. reuteri with glycerol is effective against C. difficile colonization of a complex-microbial community, whereas treatment with either glycerol or L. reuteri alone was ineffective. Co-delivery of L. reuteri and glycerol changed microbial community profiles and associated metabolites consistent with glycerol fermentation and reuterin production. Ex vivo studies showed that this combination therapy resulted in lower C. difficile burden and toxicity in stool and that this was dependent upon reuterin production. Taken together, prodrug-based adjunct therapy with probiotic L. reuteri is a viable option for preventative treatment of C. difficile infection.