Extended Data Fig. 4: Genotoxic K. oxytoca reduce abundance and diversity of Bacteroidota taxa.
(a) Boxplots compare median phylogenetic diversity values (Faith PD) for each group before infection and over time post-infection (n = 6 mice/group except day 14 and day 19 for AHC-6 and mock on day 19 where n = 5). Statistical significance was evaluated by Kruskal-Wallis (pairwise) analysis. *q < 0.05, **q < 0.01 after Benjamini-Hochberg FDR correction, (ns) not statistically significant (b) Relative abundance (%) of bacterial genera significantly amplified or suppressed by toxigenic AHC-6 on day 6 (LEfSe analysis, LDA > 2) plotted for all days as bubbles; genera of the phylum Bacteroidota are indicated (§). Alpha-diversity indices (c; Shannon) and (d; Faith PD) calculated for Bacteroidota over time shown as boxplots (n = 6 mice/group except day 6 and day 14 for AHC-6 where n = 5). Statistical significance was evaluated by Kruskal-Wallis (pairwise) analysis. *q < 0.05, after Benjamini-Hochberg FDR correction, (ns) not statistically significant. a,c,d, Boxplot center lines represent medians, box limits represent upper and lower quartiles, whiskers span min. to max. values, all points shown.
