Fig. 2
Abundance of individual bacteria carrying pathofunctions. Taxonomic affiliations of genes encoding three pathofunctions, namely, the formation of (i) trimethylamine (cutCD (a), cntAB (b), grdH (c)), (ii) the secondary bile acids lithocholic/deoxycholic acid (baiA-I (d)), and (iii) hydrogen sulfide (dsrAB (e)) were quantified in metagenomic data encompassing patients suffering from cardiovascular disease (CVD: I, II), type 2 diabetes (T2 diabetes: III–V), obesity (Obese: VI), colorectal cancer (CRC: VII-IX), liver cirrhosis (Cirr: X), and inflammatory bowel disease (IBD: ulcerative colitis (UC) and Crohn’s disease (CD), XI and XII) and compared with healthy controls. In dataset XII results of CD patients are displayed following those from UC patients, whereas CD patients of dataset XI are not shown due to the low sample size (n = 4). Taxa abundance refers to the percentage of total bacteria of a sample carrying respective genes, i.e., relative to the mean abundance of three single-copy housekeeping genes (HKG). For expression data (MTX) results are expressed relative to the mean expression of those HKG. Significant differences (*p < 0.05) and trends (+p < 0.1) between patients and healthy controls are shown (FDR-corrected Mann-Whitney U test). For CRC, “*” in healthy controls indicates significant difference (p < 0.05) from cancer patients, whereas in IBD datasets “u” and “c” refer to significantly different results (p < 0.05) in healthy controls compared with UC and CD, respectively, whereas “b” indicates the differences of both diseases from controls. The most abundant taxa that cumulatively represent 67% (a), 94% (b), 86% (c), 93% (d), and 81% (e) of total abundances of individual pathofunctions are displayed. Read similarities (S:%,) are indicated as median/first quartile protein similarities to top-hitting reference on top of each panel. §: affiliated with Enterobacteriaceae; &: affiliated with metagenomic species; Clostridium sens. str.: Clostridium sensu stricto; Clostridiales bact.: SAMEA3545284 (unclassified Clostridiales); Clost. UBA Human: Clostridiales bacteria UBA6412, UBA4701, and UBA5888; Firmicutes CAG:103: Firmicutes bacterium CAG:103; unclass Lachnosp.: unclassified Lachnospiraceae