Extended Data Fig. 1: Microbiome and metabolome diversity in germ-free and SPF mice.

a, Principal coordinate (PC) analysis of microbiome and mass-spectrometry data highlighted by sample source as germ-free (GF) or SPF (n = 4 mice in each group). The microbial signatures from the germ-free mice are an important control, which represents background reads found in buffers, tips and tubes and other experimental materials. b, Data from a highlighted by organ source (n = 4 mice in each group). c, Bray–Curtis dissimilarities of the metabolome data collected from mouse organs. The dissimilarities are calculated within individual mice of the same group (germ-free or SPF, ‘within’) or across the germ-free and SPF groups (‘GF-SPF’) (n = 4 mice in each group). Only samples collected from exact same ___location (subsection) are compared. Significance was tested with a two-sided Mann–Whitney U-test. Boxes represent the interquartile range (IQR), the notch is the 95% confidence interval of the mean, the centre is the median and whiskers are 1.5× the IQR. d, Microbiome profile of the gastrointestinal tracts of SPF mice. Data were generated by sequencing 16S rRNA gene amplicons from each organ and organ section, and analysed through the Qiita Deblur pipeline as described in the Supplementary Methods. Bacterial taxa of relevance are colour-coded according to the legend. e, Molecular network of LC–MS/MS data with nodes coloured by source as germ-free, SPF, shared or detected in blanks. Molecular families with metabolites annotated by spectral matching in GNPS are listed by a number that corresponds to the molecular family. These are level-2 or -3 annotations according to the metabolomics standards consortium¹⁶. 12-OAHSA, 12-(9Z-octadecenoyloxy)-octadecanoic acid.