Figure 3. Complex carbohydrates increase microbiome diversity and reduce K. pneumoniae colonization after antibiotic depletion.

(A–F) Mice were provided a FF or a HF diet starting on day –7, treated with oral antibiotics on day –3 to day 0 (gray shading), and gavaged with K. pneumoniae (day 0). Serial stool samples were subjected to analysis as follows: (A) Shannon α diversity of stool microbiome from mice provided a FF or HF diet including the antibiotic treatment period (gray shading) and recovery, as determined by shotgun metagenomic sequencing. (B) GH genes with significantly different abundances between FF and FH diets 4 weeks after gavage with K. pneumoniae grouped by substrate type. Open circles represent genes with higher levels in mice on the FF diet, and closed circles represent genes with higher levels in mice on the HF diet. (C) K. pneumoniae fecal CFU for mice on a FF (open circles) or HF (closed circles) diet measured 4 weeks after K. pneumoniae gavage. (D) Stool ammonia was quantified before and after antibiotic treatment (gray shading) and K. pneumoniae gavage for mice subjected to a FF (open circles) or HF (closed circles) diet. (E) Stool urea levels were quantified for mice provided a FF diet. (F) Heatmap of amino acid concentrations in mice on a FF or HF diet after colonization with K. pneumoniae. Data are presented as the mean ± SD (A–E). n = 5 mice per group. Data are representative of 2–3 independent experiments (C–F). *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001, by multiple 2-tailed t tests with Bonferroni’s correction for multiple comparisons (A, C, and D), 1-way ANOVA with Bonferroni’s correction for multiple comparisons (E), or multiple Mann-Whitney U tests with the FDR method of Benjamini, Krueger, and Yokutieli (F).