Extended Data Fig. 5: Small intestinal metabolism.
a – Log2 transformed fold changes of the mean small intestinal concentration of 42 metabolites with longitudinal patterns in the small intestine (see Fig. 3 for example profiles, Fig. 5, Supplementary Table ST4). Fold changes were calculated between male SPF and male germ-free samples in luminal content (left panel) and mucus (right panel), averaged over the 10 sampling sites and five biological replicates. Boxplots are thus based on 50 data points, where the median log2 fold change is indicated in blue, 25th and 75th percentile are denoted by the box, whiskers extend to the most extreme data points not considered outliers, and outliers are marked with the plus symbol. The grey area represents absolute log2 fold changes ≤ 2. b – Spatial metabolite profiles of luminal content or mucus concentrations in SPF and germ-free mice. Lines with shaded area indicate the moving average of the mean ± s.e.m. of concentration measurements with five male mice. Abbreviations: FC – fold change; GF – germ-free; duo – duodenum, jej – jejunum, ile – ileum, cec – cecum, and col – colon.
