Fig. 1: Antibiotic treatment significantly reduced gut commensals, increased nutrients, decreased microbial metabolites, and increased VRE growth.

a Heatmap illustrating the log2 fold change (antibiotic-treated relative to water-treated) in bacterial taxa that were significantly decreased (shown in blue) or increased (shown in red) in faecal cultures following treatment with antibiotics that promote VRE intestinal colonisation. Taxa not significantly changed with antibiotic treatment were not plotted (shown in white). n = 12 human faecal donors, Wilcoxon signed rank test (two-sided) of log-transformed abundances with Benjamini-Hochberg false discovery rate (FDR) correction, p < 0.05. b Heatmap illustrating the log2 fold change (antibiotic-treated relative to water-treated) in nutrients and metabolites that were significantly decreased (shown in blue) or increased (shown in red) in faecal cultures following treatment with antibiotics that promote VRE intestinal colonisation. Nutrients and metabolites not significantly changed with antibiotic treatment were not plotted (shown in white). n = 12 human faecal donors, Wilcoxon signed rank test (two-sided) with Benjamini-Hochberg FDR correction, p < 0.05. c, d Antibiotic treatment significantly promoted the growth of vancomycin-resistant E. faecium (NCTC 12202) and E. faecalis (NCTC 12201) in faecal microbiomes. E. faecium or E. faecalis were spiked into faecal cultures at 10³ CFU/ml (horizontal dashed line). Number of human faecal donors used in (c): Faeces + H₂O n = 8, Faeces + MTZ n = 5, Faeces + CLI n = 5, Faeces + VAN n = 6, Faeces + CRO n = 8, No faeces control n = 6. Number of human faecal donors used in (d): Faeces + H₂O n = 8, Faeces + MTZ n = 5, Faeces + CLI n = 5, Faeces + VAN n = 7, Faeces + CRO n = 7, No faeces control n = 6. Antibiotic-treated faecal culture counts (shown in red) were compared to water-treated faecal culture counts (shown in blue) using a mixed effects model (one-way) of log transformed CFU/ml with Dunnett’s multiple comparison. No faeces counts (shown in grey) were compared to water-treated faecal culture counts (shown in blue) using an unpaired t-test (two-sided) of log transformed CFU/ml. Data shown as mean ± SD. ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001. MTZ metronidazole, CLI clindamycin, VAN vancomycin, CRO ceftriaxone, TZP piperacillin/tazobactam.