Extended Data Fig. 1: Relative and absolute abundance profiles of faecal samples resuspended in sM9 or BHI and incubated with drugs.

a. Ordination plot of Bray–Curtis distances of microbial communities (ASV-level composition) in faecal samples resuspended in sM9 medium (a) or BHI medium (c) and incubated in the presence of drugs (n = 3 incubation vials per condition). Samples are coloured according to the drug amended and shaped according to the time of incubation. Please note that in (a) at T6 ENT-Hi condition two of the data points show overlapping positions in the ordination plot. sM9 medium: PERMANOVA = 0.001, R² = 0.64. BHI medium: PERMANOVA = 0.001, R² = 0.45. b. Alpha diversity metrics (number of Observed ASVs, Shannon Index, and Inverse Simpson Index) of faecal samples resuspended in sM9 medium (b) or BHI medium (d) and incubated in the presence of drugs. Each data point represents a replicate and samples from both 6 and 24 h of incubation are shown. Significant differences (p-values) determined by two-sided Wilcoxon testing are indicated, with “No drug” used as a reference group. Boxes represent the median, first and third quartile. Whiskers extend to the highest and lowest values that are within one and a half times the interquartile range. e. Total cell loads in faecal samples resuspended in BHI medium and incubated with drugs, as assessed by flow cytometry (Supplementary Table 1). **p = 0.002; unpaired two-sided t-test with “No drug” used as a reference group. Data points represent the mean value +/- SEM from three incubation vials per condition. f, g. Relative (f) and absolute (g) genus abundance profiles of microbial communities originating from faecal samples resuspended in BHI medium and incubated in the presence of drugs at T0 and after 6 or 24 h of incubation. Each bar represents the mean from triplicate incubations. All genera present at relative abundances below 0.025 or absolute abundances below 2.5x10⁷ cells.ml⁻¹ were assigned into the category “Other” (“unclass”: unclassified). Complete relative and absolute abundance profiles can be found in Supplementary Tables 3 and 4.