Fig 4.

Clindamycin induces profound, long-lasting decreases in intestinal microbial diversity. Rarefaction analyses of microbial communities in the ilea (A, B, and C) and ceca (E, F, and G) of mice that received C. difficile spores (A and E), clindamycin (B and F), or clindamycin and spores (C and G). Clindamycin was administered on day −1, and C. difficile spores were administered on day 0. The Shannon biodiversity index values of microbial communities in the ileum (D) and cecum (H) were also calculated at the time points indicated. Untreated, C. difficile-inoculated mice were only measured on days 1, 7, 14, and 21. Panels A, B, C, E, F, and G and panels D and H, respectively, share keys.