a, Molecular network of MS/MS data from synthesized amino acid conjugated bile acids and the duodenum of SPF mice. LC–MS/MS data from synthetic standards were networked with mouse samples and spectral matching. Molecular networking is indicated by node colouring. Mirror plots show the alignment between the mouse and the synthetic standards. Nodes shaped as arrowheads had hits in the GNPS libraries, and node size is scaled to the spectral count. Tauro, taurocholic acid. These experiments were performed twice. b, Three-dimensional molecular cartography of the mean abundance of the newly discovered conjugates mapped onto a 3D-rendered model of the mouse gastrointestinal tract, as a heat map according to the colour scale. Organs are labelled as described in Fig. 1. c, Molecular network of conjugated bile acids from portal and peripheral blood of germ-free and SPF mice. Nodes are coloured by source as germ-free portal, germ-free portal and peripheral blood, SPF portal and peripheral blood, GF portal and peripheral blood and SPF peripheral blood, and all. Arrowhead nodes represent known compounds in the GNPS spectral database; circular nodes represent unknown compounds. The annotations were obtained through spectral matches against reference libraries (level two or three16). d, Mean area-under-the-curve abundance and s.d. of bile acids of interest during incubation with an actively growing batch human faecal culture for 24 h (n = 3 independent incubations). e, Molecular network of newly identified conjugated bile acids after incubation in a human faecal batch culture experiment. Each node represents a unique tandem mass spectrum; arrowhead-shaped nodes indicate known spectra in the GNPS database. The nodes are coloured by their retention time according to the legend, and the mass shifts between nodes are mapped onto the edge representing the cosine connection between related spectra. The H 2 mass shift representing oxidation of the newly identified conjugates is shown. f, Mean ion intensity and s.d. of the oxidized forms of Phe-chol, Tyr-chol and Leu-chol through the 24-h batch faecal culture incubation (n = 3 independent incubations).