Fig. 1: Biogeography of the male SPF mouse metabolome.
a, Hierarchical clustering analysis of metabolite abundances from luminal content samples of male SPF mice. Abundances for all 128 quantified metabolites are shown as z score normalized concentrations, averaged from five mice, across the 15 sampling sites. Clustering based on Euclidian distance identified three main clusters corresponding to the three main physiological regions of the digestive tract: stomach, small intestine and large intestine. Metabolites are colour-coded according to MetaCyc (bottom right). b, PCA of metabolite concentrations from individual male SPF mice based on all 150 luminal and mucus samples covering the entire intestine. PCA was performed on z score normalized metabolite concentrations, with five mice per sample. Colours indicate sites grouped by intestinal region, symbols indicate lumen or mucus and the large intestine content cluster is highlighted in grey. c, Differential analysis of metabolite concentrations between luminal content and mucus samples. Concentrations were averaged across all 15 sampling sites for five male mice within the respective habitat. Positive or negative fold changes indicate higher concentrations in lumen or mucus, respectively. P values were calculated using a two-sided paired-sample Student’s t-test with Benjamini–Hochberg correction for multiple testing and are displayed as −log10 transformed. Metabolites with significantly differing concentrations (absolute log2(fold change) ≥ 1.5, corrected P ≤ 0.05) are coloured according to the MetaCyc classification, as defined in the box below. Lumen and mucus sampling types are represented schematically on the left, aligned to the corresponding parts of the volcano plot. Abbreviations: FC, fold change.
