Extended Data Figure 8: 16S rRNA-based comparison of faecal bacterial communities in mice obtained from Envigo and CRL and mice of different genetic backgrounds from a common vendor.
From: Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist
a, C3H/HeN mice were treated with M4284 (100 mg kg−1, three doses over 24 h), vehicle alone (10% cyclodextrin, three doses over 24 h), or ciprofloxacin (15 mg kg−1, two doses over 24 h). Untreated mice served as reference controls. Heat maps show the effect of each of the treatments on animals from CRL and Envigo. Each row represents a species-level bacterial taxon, while each column represents a mouse sampled 24 h after the termination of the indicated treatment. Coloured boxes next to the taxon names indicate species whose relative abundance was significantly changed by ciprofloxacin treatment (P < 0.05; Wilcoxon signed-rank test with false discovery rate (FDR) correction). Individual comparisons between untreated and other treatment types did not disclose changes that were statistically significant by Wilcoxon signed-rank test with FDR correction. b, Corresponding faecal samples collected 24 h after treatments (as shown in Extended Data Fig. 8a) were homogenized, diluted serially, and plated on MacConkey medium. The abundance of bacteria capable of growing on the selective medium was similar between faecal samples taken from untreated mice and those collected 24 h after treatment with cyclodextrin and M4284. No colonies were detected from faecal samples collected 24 h after ciprofloxacin treatment. c, Comparison of the representation of bacterial taxa in the faecal microbiota of untreated mice obtained from different vendors or representing different genetic backgrounds. Each row in the heat map represents a species-level taxon, while each column represents a mouse of the indicated genetic background from the indicated vendor. Coloured boxes indicate species whose relative abundances were significantly different (P < 0.05) between all three groups of animals (Kruskal–Wallis test with FDR correction). Rows of each heat map were hierarchically clustered according to pair-wise distances using Pearson correlation. n = 5 mice per treatment type, 1 biological replicate (a); n = 5 mice, 1 biological replicate (b); n = 5 mice per vendor/mouse strain, 1 biological replicate (c). Bars denote median. **P < 0.001, Mann–Whitney U test (b).
