DOI: 10.6084/m9.figshare.31347121
title: Data published in the thesis - Chapter 3

description: In this item, you can find all supplementary tables and figures as described in the <b>Chapter 3</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 "Figure3-S1" represents supplementary figure 1 from chapter 3.</i><b>Figure3-S1</b>.<b> </b>Patients treated with IFX and ADA have similar baseline colonic mucosal microbiome.<b> </b>Alpha diversity measured by Shannon and Simpson indices at amplicon sequence variant (ASV) level. Wilcoxon signed-rank test. Principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarity at ASV level, illustrating beta diversity between responders and non-responders. Permutational multivariate analysis of variance (PERMANOVA).<b>Figure3-S2</b>. <i>M. gnavus </i>and <i>Blautia </i>share similar patters in baseline colonic mucosal microbiome of patients treated with IFX and ADA. Differential analysis of the relative abundance of the 15 most predictive ASVs from the anti-TNFα – colon model (<b>Figure 5B</b>) between responders and non-responders to adalimumab (ADA; n = 13 responders, n = 10 non-responders) and infliximab (IFX; n = 9 responders, n = 6 non-responders). Comparisons were performed using the Mann-Whitney U test separately for each medication. For ADA, four ASVs showed significantly different relative abundances between responders and non-responders and are displayed in the upper panel. For IFX, no comparisons reached statistical significance; the corresponding dot plots are shown in the lower panel.<b>Table3-S1</b>. Baseline clinical characteristics of patients treated with vedolizumab. Values are median (interquartile range) unless otherwise defined. The number of missing data is shown in square brackets. Percentages have been calculated in the available data. Anti-TNFα: infliximab & adalimumab; HBI: Harvey Bradshaw Index; SES-CD: simple endoscopic disease activity score; Immunomodulator: azathioprine, mercaptopurine, thioguanine, methotrexate.<b>Table3-S2</b>. Baseline clinical characteristics of patients treated with ustekinumab. Values are median (interquartile range) unless otherwise defined. The number of missing data is shown in square brackets. Percentages have been calculated in the available data. Anti-TNFα: infliximab & adalimumab; HBI: Harvey Bradshaw Index; SES-CD: simple endoscopic disease activity score; Immunomodulator: azathioprine, mercaptopurine, thioguanine, methotrexate.<b>Table3-S3</b>. Complete list of ASVs identified in colonic and ileal biopsies from Crohn’s disease patients included in this study. ASVs are listed in alphabetical order based on their representative sequences.<b>Table3-S4</b>. List of ASVs annotated as host-associated eukaryotes or of unknown origin, and therefore excluded from downstream analysis. This table represents a subset of ASVs listed in Table S3.<b>Table3-S5</b>. Euclidean distances between the centroids of the three intervention cohorts.<b>Table3-S6</b>. Alpha diversity metrics in colonic (left) and ileal (right) biopsies from Crohn’s disease patients treated with anti-TNFα, vedolizumab (VDZ), or ustekinumab (USTE). Metrics include Observed richness, Shannon index, Simpson index, and Fisher’s alpha using the amplicon sequence variant (ASV)-level count table. Comparisons between responders and non-responders within each treatment group were performed using the Wilcoxon rank-sum test. Reported values include the W statistic, <i>P-value</i>, and 95% confidence interval (CI) of the difference in medians.<b>Table3-S7</b>. Beta diversity analysis in colonic (left) and ileal (right) biopsies from Crohn’s disease patients treated with anti-TNFα, vedolizumab (VDZ), or ustekinumab (USTE). Principal coordinates analysis (PCoA) was performed based on Bray–Curtis dissimilarity (BCD), unweighted UniFrac distance (UUD), and weighted UniFrac distance (WUD) matrices at amplicon sequence variant (ASV) level. Comparisons between responders and non-responders were assessed using permutational multivariate analysis of variance. Reported values include degrees of freedom (Df), R², F statistic (F-model), and <i>P-value</i>.<b>Table3-S8</b>. Performance metrics of six extra trees-based models (i–vi) predicting treatment response in Crohn’s disease. Columns include: Model (identifier), Sub-cohort (treatment type and biopsy location, e.g., anti-TNFα - colon, VDZ - ileum), Area Under the Curve (AUC) of each model, and P-value assessing model significance. P-values were calculated by comparing extra trees-based model performance to 200 randomly generated models with permuted response labels to evaluate overfitting.<b>Table3-S9</b>. List of the 15 most informative ASVs from colonic biopsies distinguishing responders and non-responders to anti-TNFα therapy. This table represents a subset of ASVs listed in Table S3. Columns include: ASV_ID (amplicon sequence variant identifier), Representative sequence, Feature importance (from the extra trees-based model), SILVA 132 Taxonomy (Family | Genus | Species) assigned by metabarcoding, Higher (indicating association with response or non-response), and BLASTN results including Query cover (%) and Percent identity (%). Manual BLASTN was performed only if genus-level taxonomy was unavailable or needed further confirmation; otherwise, BLASTN columns are left empty.<br>