DOI: 10.6084/m9.figshare.31347169
title: Data published in the thesis - Chapter 4

description: In this item, you can find all supplementary tables as described in the <b>Chapter 4</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>Tables are prefixed by the chapter. For example "Table4-S1" represents supplementary table 1 from chapter 4.</i><b>Table4-S1</b>. Microbiome covariates in CRC patients. 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 354 patients with complete data availability. NA, not applicable.<b>Table4-S2</b>. Faecal microbial β-diversity in CRC patients undergoing colorectal surgery. Beta diversity was evaluated at the amplicon sequence variants (ASV) and genus levels using the Bray-Curtis dissimilarity index, weighted and unweighted UniFrac distance matrices. The impact of AL on microbial composition was assessed using the permutation multivariate analysis of variance (PERMANOVA) test within each clinical study (SANICSII, n = 49; REVEAL, n = 370) and in the combined cohort. NA, not applicable.<b>Table4-S3</b>. Association between Prevotellaceae taxa and principal coordinates. Spearman rho correlation was assessed between the relative abundance of Prevotellaceae taxa (<i>Prevotella</i> 2, <i>Prevotella</i> 7, <i>Prevotella</i> 9, Prevotellaceae NK3B31 group, <i>Alloprevotella</i>, and <i>Paraprevotella</i>) and the first two principal coordinates (PCoA1 and PCoA2) of the microbial composition in our CRC cohort.<b>Table4-S4</b>. Clinical characteristics of CRC patients included in the shotgun metagenomic sequencing analysis. Values are presented as mean (SD) or median (IQR: Q1-Q3) for non-normally distributed, unless otherwise specified. Missing data are indicated in square brackets. Percentages are calculated based on available data. Differences among AL, AH<sup><em>S.copri</em></sup><sup>-High</sup> and AH<sup><em>S.copri</em></sup><sup>-Zero</sup> patients were assessed using the non-parametric Kruskal-Wallis test for numerical variables, with subsequent pairwise comparisons adjusted for multiple testing using the Bonferroni method. Categorical variables were analysed using the Chi-square test. Note:<sup> </sup><sup>a </sup>indicates <i>P</i> = 0.004 between AL and AH<sup><em>S.copri</em></sup><sup>-High</sup>. NA, not applicable; M, male; F, female.<br><b>Table4-S5</b>. List of KOs with higher relative gene abundance in AL compared to both AH subgroups.<b>Table4-S6</b>. List of KOs associated with quorum-sensing (QS) and two-component systems (TCS) enriched in AL compared to AH subgroups. KOs are organized by comparison: AL vs. AH<sup><em>S.copri</em></sup><sup>-Zero</sup> and AL vs. AH<sup><em>S.copri</em></sup><sup>-High</sup>. KOs associated with QS that show higher relative gene abundance in AL in both comparisons are highlighted in yellow. KOs associated with two-component systems that show higher relative gene abundance in AL in both comparisons are highlighted in orange.<b>Table4-S7</b>. Clinical characteristics of CRC patients included in the measurement of plasma markers. Values are presented as mean (SD) or median (IQR: Q1-Q3) for non-normally distributed, unless otherwise specified. Missing data are indicated in square brackets. Percentages are calculated based on available data. Differences in numerical variables between AL and AH patients were assessed using Student’s t-test or Mann-Whitney U for non-normally distributed. Differences in categorical variables were assessed using the Chi-square test. NA, not applicable; M, male; F, female.<b>Table4-S8</b>. Spearman rho associations between the preoperative faecal relative abundance of <i>S. copri</i> and postoperative day 3 (POD3) plasma marker levels. IL6, interleukin-6; PTX3, pentraxin-3; IFNγ, interferon-γ.<b>Table4-S9</b>. Forward and reverse sequences of the primers used in the <i>in vivo</i> experiment.<br>