Fig. 4

Assessment of microbiota composition after vancomycin or colistin antibiotic treatment. a Relative abundance (% reads) of gram-positive Ruminococcaceae and Lachnospiraceae in the feces of mice treated with colistin, vancomycin, or vehicle at day 0 prior DSS. b Relative abundance (% reads) of Enterobacteriaceae in the feces of mice treated with colistin compared to untreated mice at day 0. c Bacterial-taxon-based analysis at the phylum level in the feces of mice treated with colistin, vancomycin, and vehicle. d Shannon index, describing the alpha diversity of the bacterial microbiota (16S) in the fecal microbiota of mice treated with vancomycin (V), colistin (C), and vehicle (H₂O). e Enterobacteriaceae levels (CFU/mg of feces) in the feces of mice treated with colistin compared to those of untreated mice. f Beta diversity. Principal coordinate analysis of Bray–Curtis distance with each sample colored according to the disease phenotype. PC1, PC2, and PC3 represent the top three principal coordinates that captured most of the diversity. The fraction of diversity captured by the coordinate is given as a percentage. Groups were compared using PERMANOVA. Throughout, data are presented as the mean ± s.e.m. *P < 0.05, **P < 0.01, and ***P < 0.001 by one-way ANOVA with a post hoc Tukey test; n = 5 mice per group