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Background  Colonization by the pathogen  Clostridium difficile  often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring resistance to invasion by  C. difficile  is desirable because diagnostic and therapeutic strategies based on the human microbiota have the potential to provide more precision to the management and treatment of  Clostridium difficile  infection (CDI) and its recurrence.    Methods  We conducted a longitudinal study of adult patients diagnosed with their first CDI. We investigated the dynamics of the gut microbiota during antibiotic treatment, and we used microbial or demographic features at the time of diagnosis, or after treatment, to predict CDI recurrence. To check the validity of the predictions, a meta-analysis using a previously published dataset was performed.    Results  We observed that patients’ microbiota “before” antibiotic treatment was predictive of disease relapse, but surprisingly, post-antibiotic microbial community is indistinguishable between patients that recur or not. At the individual OTU level, we identified  Veillonella dispar  as a candidate organism for preventing CDI recurrence; however, we did not detect a corresponding signal in the conducted meta-analysis.    Conclusion  Although in our patient population, a candidate organism was identified for negatively predicting CDI recurrence, results suggest the need for larger cohort studies that include patients with diverse demographic characteristics to generalize species that robustly confer colonization resistance against  C. difficile  and accurately predict disease relapse.    Electronic supplementary material  The online version of this article (10.1186/s40168-017-0368-1) contains supplementary material, which is available to authorized users.

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment