DOI: 10.6084/m9.figshare.31347007
title: Data published in the thesis - Chapter 2

description: In this item, you can find all supplementary tables and figures as described in the <b>Chapter 2</b> of the thesis entitled "The role of the gut microbiome in intestinal wound healing: Uncovering microbial insights from inflammatory bowel disease and colorectal cancer".<b>Legends:</b><i>Figures and tables are prefixed by the chapter. For example "Figure2-S1" represents supplementary figure 1 from chapter 2.</i><b>Figure2-S1</b>. Mechanical bowel preparation does not influence Jaccard distances between sampling sites. Jaccard distances between samples collected from different sites within the same participant, stratified by mechanical bowel preparation status. Left panel: patients without mechanical bowel preparation. Right panel: patients who received mechanical bowel preparation. Distances were calculated between matched sampling sites from the same individual. ANOVA; Tukey post-hoc comparison. For all panels: ^ <i>P</i> &lt; 0.10; * <i>P</i> &lt; 0.05; ** <i>P</i> &lt; 0.01; *** <i>P</i> &lt; 0.001. <b>Table2-S1</b>. Microbiome covariates. The individual effect of each clinical patient characteristic was assessed using Capscale analysis, while cumulative effects were evaluated with forward stepwise distance-based redundancy analysis. The analysis was performed for 60 patients who provided 3 samples per patient, consisting a complete set of 180 samples. NA, not applicable. <b>Table2-S2</b>. Alpha diversity metrics of faecal and mucosal microbiota. Observed richness and Shannon index calculated at ASV and genus level. Differences between sampling sites (RT, MS and FS) were assessed using a non-parametric repeated-measures Friedman test, accounting for subject identifier, followed by post hoc pairwise comparisons using Wilcoxon signed-rank tests. <b>Table2-S3</b>. Beta diversity of faecal and mucosal microbiota. Beta diversity was assessed using Bray-Curtis dissimilarity at ASV and genus level, and unweighted and weighted UniFrac distances at ASV level. Differences between sampling sites (RT, MS and FS) were evaluated using PERMANOVA, accounting for subject identifier, followed by post hoc pairwise PERMANOVA comparisons. NA, not applicable. <b>Table2-S4</b>. Differential abundance analysis between RT and MS samples at genus level. Results (<i>P-adjusted</i> &lt; 0.05) from DESeq2 analysis comparing resected tissue (RT) and mucosal swabs (MS). Fold changes and adjusted P-values are shown for each genus. <b>Table2-S5</b>. Differential abundance analysis between RT and MS samples at ASV level. Results (<i>P-adjusted</i> &lt; 0.05) from SIAMCAT analysis comparing resected tissue (RT) and mucosal swabs (MS). Generalized fold changes and adjusted <i>P-values</i> are shown for each ASV. <b>Table2-S6</b>. Clinical metadata of patients per sampling location. Patient characteristics stratified by gastrointestinal location: right colon (n=25), left colon (n=17), and rectum (n=18). Values are presented as mean (standard deviation) or median (Q1-Q3) for non-normally distributed, unless otherwise specified. Missing data are indicated in square brackets. Percentages are calculated based on available data. a; <i>P</i> = 0.038 between Right colon and Rectum.