Fig. 4

Changes to the gut microbiome largely persist following dox washout. Analysis of gut microbiome from stool samples collected at 6 and 12 wk of age, assessing the effect of time in untreated mice and of drug washout in dox-treated mice. A, B Observed OTUs (left) and Simpson index (right) as a function of age in untreated mice and of drug washout in dox-treated mice. Observed OTUs are unaffected by time and washout, while Simpson is increased in Tg mice both with age and drug removal. (A, WT; B, Tg). C, D PCoA plots of weighted UniFrac distances show that the overlap in species (β-diversity) was changed by drug washout for Tg mice but not WT, while neither genotype is altered by age alone (C, WT; D, Tg). E, F Relative abundance of bacterial taxa was unchanged by age alone (limited to taxa with average abundance ≥ 0.05% across all samples); only one phylum increased significantly upon drug washout in Tg mice (E, WT; F, Tg). Statistical testing: Kruskal–Wallis (A, B), PERMANOVA (C, D), and Mann–Whitney U, reporting FDR-adjusted p-value (E, F). n = 5–7 mice/group. *p < 0.05. Red and blue = dox-treated Tg and WT, respectively; grey and white = untreated Tg and WT, respectively