Figure 1.

Vancomycin induces persistent changes in the structure and richness of the human microbiota. Patients received vancomycin treatment for 2 weeks (T, vancomycin treated) or did not receive vancomycin (C, control group). Faecal samples were obtained immediately before treatment (Baseline), the day of antibiotic cessation (Vanco), and 2, 6, 14 and 22 weeks (w) after antibiotic cessation (Recovery). As control, faecal samples from patients that did not receive vancomycin were obtained at similar timepoints. (a) Hierarchical clustering based on microbiota similarity (see the supplementary methods) among the faecal samples analysed from vancomycin-treated and control patients. Samples with a more similar microbiota are clustered within the same branch of the tree. Colours indicate the time frame where the faecal sample was obtained. Numbers indicate the patient ID. Those samples obtained at the last timepoint (22 weeks post-antibiotic withdrawal) are labelled with asterisks. (b) Number of OTUs (a close estimate of bacterial species) and (c) Shannon index of microbial diversity calculated from the microbiota of faecal samples collected at baseline and at different timepoints after vancomycin treatment. For comparison, the same indices were calculated from the faecal samples collected at similar timepoints from patients who did not receive vancomycin (control). Bar graphs represent mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. ns, not significant. n = 5–12 per group and timepoint except for the second timepoint from control patients where n = 3. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.