Fig. 5. Changes in the fecal concentration of bile acids and biomarkers for Bilophila on the animal-based diet.

(A) Deoxycholic acid, a secondary bile acid known to promote DNA damage and hepatic carcinomas²⁶, accumulates significantly on the animal-based diet (p<0.01, two-sided Wilcoxon signed-rank test; see Supplementary Table 23 for the diet response of other secondary bile acids). (B) RNA-Seq data also supports increased microbial metabolism of bile acids on the animal-based diet, as we observe significantly increased expression of microbial bile salt hydrolases (K01442) during that diet arm (q<0.05, Kruskal-Wallis test; normalized to reads per kilobase per million mapped, or RPKM; n=8–21 samples/diet arm). (C) Total fecal bile acid concentrations also increase significantly on the animal-based diet, relative to the preceding baseline period (p<0.05, two-sided Wilcoxon signed-rank test), but do not change on the plant-based diet (Extended Data Fig. 9). Bile acids have been shown to cause IBD in mice by stimulating the growth of the bacterium Bilophila⁶, which is known to reduce sulfite to hydrogen sulfide via the sulfite reductase enzyme (dsrA; Extended Data Fig. 10). (D) Quantitative PCR showed a significant increase in microbial DNA coding for dsrA on the animal-based diet (p<0.05; two-sided Wilcoxon signed-rank test), and (E) RNA-Seq identified a significant increase in sulfite reductase expression (q<0.05, Kruskal-Wallis test; n=8–21 samples/diet arm). Barplots (B,E) display mean±sem.