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While the knowledge on gut microbiota -  C. difficile  interactions has improved over the years, the understanding of the underlying mechanisms providing colonization resistance as well as preventative measures against the infection remain incomplete. In this study the antibiotic clindamycin and polyphenol extracts from pomegranate and blueberries were used individually and in combination to modulate fecal microbial communities in minibioreactor arrays (MBRA). Modulated communities were inoculated with  C. difficile  (ribotype 027). Subsequent 7-day periodical monitoring included evaluation of  C. difficile  growth and activity of toxins TcdA and TcdB as well as analysis of MBRA bacterial community structure (V3V4 16 S metagenomics). Polyphenols affected multiple commensal bacterial groups and showed different synergistic and antagonistic effects in combination with clindamycin. Exposure to either clindamycin or polyphenols led to the loss of colonization resistance against  C. difficile . The successful growth of  C. difficile  was most significantly correlated with the decrease in  Collinsella  and  Lachnospiraceae . Additionally, we demonstrated that  Clostridium sporogenes  decreased the activity of both  C. difficile  toxins TcdA and TcdB. The feature was shown to be common among distinct  C. sporogenes  strains and could potentially be applicable as a non-antibiotic agent for the alleviation of  C. difficile  infection.

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Microbiota in vitro modulated with polyphenols shows decreased colonization resistance against Clostridioides difficile but can neutralize cytotoxicity