Extended Data Fig. 8: Microbial bile salt hydrolase genes exhibited similar abundance and diversity in intestinal and stool samples despite differences in conjugated bile acids along the intestinal tract.
From: Profiling the human intestinal environment under physiological conditions
a) Open reading frames identified as bile salt (cholylglycine) hydrolase (BSH) enzymes via a hidden Markov model (HMM) search, normalized by the total number of open reading frames detected in the sample. b) The distribution of rank coverage of bsh genes was similar between intestinal and stool samples. c) Rank coverages of bsh genes in devices of each type and in stool are similar. (all P > 0.90). d) Percentage of primary (hydroxylated) bile acids was similar across device types and was lower in stool compared with intestinal samples (top to bottom: P = 3.7 × 10−13, 1.3 × 10−10, and 0.91). e) Glycocholic acid (GCA) concentration decreased along the intestinal tract (top to bottom: P = 1.6 × 10−12, 0.035, and 0.003). f) The log2(ASV count) of Alistipes putredinis, Anaerostipes hadrus, and Bilophila wadsworthia was negatively correlated (Spearman; P = 0.0068, 0.0004, and 0.0068 in devices and P = 0.63, 0.84, and 0.70 in stool, respectively) with log10(GCA concentration). Only ASVs with P < 0.01 after a Benjamini-Hochberg correction in device samples are shown. g) Taurochenodeoxycholic acid (TCDCA) concentration decreased along the intestinal tract (top to bottom: P = 0.0070, 1.9 × 10−4, 4.2 × 10−6, 1.5 × 10−10, and 0.0020). h) log2(ASV read count) of Alistipes putredinis and Bilophila wadsworthia in devices was negatively correlated (Spearman; P = 2.5 × 10−5 and 3.3 × 10−7, respectively) with log10(TCDCA concentration). Only ASVs with P < 0.01 after a Benjamini-Hochberg correction in device samples are shown. i) log2(ASV read count) of Bilophila wadsworthia in devices was negatively correlated (Spearman; P = 2.4 × 10−5) with log10(concentration of taurodeoxycholic acid (TDCA)). Only ASVs with P < 0.01 after a Benjamini-Hochberg correction in device samples are shown. In (a–c), n = 175 device and n = 58 stool samples were used for analysis. In (d–h), n = 210 device samples and n = 56 stool samples were used for analysis. All boxplots show the median and 1st and 3rd quartiles. ns: not significant, ****: P ≤ 0.0001, Bonferroni-corrected two-sided Wilcoxon rank-sum test. Bile acids shown are log10-transformed concentrations in units of ng/mL or ng/g for intestinal or stool samples, respectively.
