Fig. 6

Intra-individual similarity of the microbiota in patients with or without recurrent C. difficile infection. The microbial community similarity within patients was compared using the Yue and Clayton dissimilarity index (θ _YC ). a Intra-individual similarity was lower in patients with recurrence compared with patients without recurrence or reinfected with C. difficile (Kruskal–Wallis test, p = 0.025). b Microbial community similarity of the index sample from a patient was compared with different stages of clinical diagnosis in nonrecurrent, recurrent, and reinfected patients: to recovery (nonrecurrent, non-reinfected samples >14 days of a positive sample), to recurrence (subsequent positive sample within 14–56 days), reinfection (subsequent positive sample >56 days), and during treatment (sample collected within 14 days of a positive sample) (Kruskal–Wallis, not significant). ns not significant