Fig. 3

Co-occurrence analysis of individual pathofunctions. Analyses were performed on abundance data derived from 12 datasets (Table 2). Datasets IV and VI were merged as they derived from one source and have overlapping samples in the healthy control group. Only metagenomic results of datasets XII and XIII were considered. Edge-width represents correlation strength defined as the number of datasets displaying a correlation (p and q < 0.05 and Spearman’s rho > 0.35; a minimum of three correlations was required for connecting individual nodes), and node sizes reflect median abundances. Abundances of genes encoding the formation of (i) trimethylamine (cutCD (orange), cntAB (red), grdH (pink)), (ii) the secondary bile acids lithocholic/deoxycholic acid (baiA-I (black)), and (iii) hydrogen sulfide (dsrAB (blue)) are shown in (a). In (b), gene abundances of individual carriers are depicted with taxa affiliated with Enterobacteriaceae, underlined. &: affiliated with metagenomic species; Clostridium sensu. str.: Clostridium sensu stricto; Clostridiales bact.: SAMEA3545284 (unclassified Clostridiales); UBA Human: Clostridiales bacteria UBA6412, UBA4701, and UBA5888; Firmicutes CAG:103: Firmicutes bacterium CAG:103; unclass Lachnosp.: unclassified Lachnospiraceae