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Clostridium difficile  infection (CDI) is typically associated with disturbed gut microbiota and changes related to decreased colonization resistance against  C. difficile  are well described. However, nothing is known about possible effects of  C. difficile  on gut microbiota restoration during or after CDI. In this study, we have mimicked such a situation by using  C. difficile  conditioned medium of six different  C. difficile  strains belonging to PCR ribotypes 027 and 014/020 for cultivation of fecal microbiota. A marked decrease of microbial diversity was observed in conditioned medium of both tested ribotypes. The majority of differences occurred within the phylum  Firmicutes , with a general decrease of gut commensals with putative protective functions (i.e.  Lactobacillus ,  Clostridium_XIVa ) and an increase in opportunistic pathogens (i.e.  Enterococcus ). Bacterial populations in conditioned medium differed between the two  C. difficile  ribotypes, 027 and 014/020 and are likely associated with nutrient availability. Fecal microbiota cultivated in medium conditioned by  E. coli ,  Salmonella  Enteritidis or  Staphylococcus epidermidis  grouped together and was clearly different from microbiota cultivated in  C. difficile  conditioned medium suggesting that  C. difficile  effects are specific. Our results show that the changes observed in microbiota of CDI patients are partially directly influenced by  C. difficile .

Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure