Supplementary Figure 4.

Endoscopically visible biofilms consist of dense bacterial agglomerations independent of disease. (A–H) Comparison between BF⁺ biopsies (orange) and BF^– biopsies (blue), separated for disease cohort (same patients as Figure 1). (I) Description of biopsy locations: BF⁺ biopsies (orange) were taken from areas in the cecum or ascending colon with endoscopically visible biofilm, BF^– biopsies (blue) were taken in the same area of BF^– patients. Distal-Bx (biopsies) (yellow) were taken from BF⁺ patients in distal areas without endoscopically visible biofilms. (J–R) Same samples as for Supplementary Figure 4A–H with addition of data from Distal-Bx (yellow). (A, J) Total number of bacteria normalized to length of epithelium per section. (B, K) Maximum density of bacteria in one 144.7 × 144.7 μm confocal microscopy image per section. (C, L) Maximum width of methacarn-fixed H&E surface layer on top of epithelium in each section. (D, M) Ratio of quantitative polymerase chain reaction determined 16S rRNA gene copies to total DNA of biopsies. (E, N) Number of bacteria 3 μm from the epithelium, normalized to length of epithelium per section. (F, O) Maximum density of bacteria up to 3 μm distal from the epithelium in one 144 × 144 μm confocal microscopy image per section. (G, P) Maximum width of methacarn-fixed PAS surface layer on top of epithelium per section. (H, Q) Average width of methacarn-fixed PAS-stained surface layer on top of epithelium per section. (R) Percentage of biopsies with more than 10⁹ · mL^–1 bacteria invading the mucus layer in at least one 144.7 × 144.7 μm confocal microscopy image. (S) Correlation matrix with Pearson correlation coefficients of microscopic data of BF⁺ biopsies and BF^– biopsies, P values ≤ .05 have been colored. (T) Location of endoscopically visible biofilms in IBS, UC, and controls. ∗P ≤ .05; ∗∗P ≤ 0.01; ∗∗∗P ≤ .001. (A, B, E, F, J, K, N, O) Zero values are displayed in direct contact with the x-axis, as they are not defined on a log-scale. (A–C, E, F, J–L, N, O) Kruskal-Wallis test with Dunn’s multiple comparison test, (D, G, H, M, P, Q) 1-way analysis of variance with Turkey’s multiple comparison test on log-transformed data, (R) Fisher exact test with Bonferroni correction for multiple comparisons. (A–C, E–L, N–S) n = 37 BF⁺, n = 47 BF^–, n = 30 Distal-Bx (D, M) n = 42 BF⁺, n = 56 BF^–, n = 35 Distal-Bx.