Fig. 1: Fibre deprivation leads to microbiota-mediated mucosal barrier breakdown.

Mice were fed an FR (green dots) or an FF (red dots) diet for 40 days. a, Differential abundance analysis of taxa in the faeces of FR-fed mice (green bar) versus FF-fed mice (red bar) (n = 10 mice per group, 5 mice per cage, Wald test, P values adjusted using the Benjamini–Hochberg method, features with less than 1 count on average across all samples were excluded). Data are presented as mean ± s.e.m. Taxa in bold depict known/potential mucin-degrading bacteria; for Akkermansia, ~1.78-fold increase in FF- compared with FR-fed mice (change from average relative abundance of 1.7% to 5.7%). b, Representative images of Alcian blue-stained longitudinal colonic sections of mice fed an FR or FF diet for 40 days. Black arrowheads indicate the edges of the mucus layer (n = 5 mice per group) c, Mucus layer thickness measured on colonic section stained with Alcian blue. Each dot is the average of several measurements from one animal (n = 5 mice per group, two-tailed Mann–Whitney test). The average number of measurements per mouse is indicated on the X axis. d, Colonic mucus layer penetrability to 1-μm-sized beads. Each dot is an average of 4–7 measurements from one animal (n = 10 mice per group, two independent experiments). e, Goblet cell counts per crypt. Each dot is the average of multiple measurements from one animal (n = 5 mice per group). f, Intestinal permeability to FITC-dextran (n = 8–9 mice per group, two independent experiments, two-tailed Mann–Whitney test). g–j, Relative transcript levels of Il25 (g), Il33 (h), Ifng (i) and Tnfa (j) mRNA in the colon, caecum and ileum. Expression levels were normalized to the FR group, independently for each tissue (n = 5–10 mice per group, two independent experiments, multiple Mann–Whitney, P values adjusted using the Benjamini–Hochberg method). Each dot represents one mouse. All dot plots are represented with mean ± s.e.m.