Data published in the thesis - Chapter 2

In this item, you can find all supplementary tables and figures as described in the Chapter 2 of the thesis entitled "The role of the gut microbiome in intestinal wound healing: Uncovering microbial insights from inflammatory bowel disease and colorectal cancer".Legends:Figures and tables are prefixed by the chapter. For example "Figure2-S1" represents supplementary figure 1 from chapter 2.Figure2-S1. 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: ^ P P P P Table2-S1. 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. Table2-S2. 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. Table2-S3. 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. Table2-S4. Differential abundance analysis between RT and MS samples at genus level. Results (P-adjusted Table2-S5. Differential abundance analysis between RT and MS samples at ASV level. Results (P-adjusted P-values are shown for each ASV. Table2-S6. 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; P = 0.038 between Right colon and Rectum.本数据集包含题为《肠道菌群在肠道伤口愈合中的作用：从炎症性肠病与结直肠癌中挖掘微生物组研究洞见》的论文第二章中提及的全部补充表格与附图。 图例说明：所有图表与表格均以所属章节作为编号前缀。例如，"Figure2-S1"代表第二章的第1幅补充附图。 Figure2-S1：机械肠道准备不影响不同采样位点间的雅卡德距离（Jaccard distances）。该图展示了同一名受试者不同采样位点样本间的雅卡德距离，并按机械肠道准备状态进行分层。左面板为未接受机械肠道准备的患者数据，右面板为接受机械肠道准备的患者数据。距离计算基于同一受试者的配对采样位点，统计方法采用方差分析（Analysis of Variance, ANOVA）与图基事后多重比较（Tukey post-hoc comparison）。所有面板中：^ P P P P Table2-S1：微生物组协变量。本研究通过约束主坐标分析（Capscale）评估每项临床患者特征的独立效应，并采用基于距离的冗余分析正向逐步回归法评估累积效应。分析对象为60名患者，每名患者提供3份样本，总计完整样本量180份。NA表示不适用（not applicable）。 Table2-S2：粪便与黏膜微生物组的α多样性指标。分别在扩增子序列变异（Amplicon Sequence Variant, ASV）与属水平计算观测丰富度（Observed richness）与香农指数（Shannon index）。采样位点（RT, MS, FS）间的差异采用考虑受试者标识的非参数重复测量弗里德曼（Friedman）检验进行评估，随后采用威尔科克森符号秩检验进行事后两两比较。 Table2-S3：粪便与黏膜微生物组的β多样性。β多样性分析采用布雷-柯蒂斯相异度（Bray-Curtis dissimilarity，在ASV与属水平），以及ASV水平的未加权与加权UniFrac距离。采样位点（RT, MS, FS）间的差异采用考虑受试者标识的置换多元方差分析（PERMANOVA）进行评估，随后进行事后两两置换多元方差分析比较。NA表示不适用。 Table2-S4：属水平下RT与MS样本间的差异丰度分析。结果（校正后P值） Table2-S5：ASV水平下RT与MS样本间的差异丰度分析。结果（校正后P值为每个ASV展示） Table2-S6：不同采样位置患者的临床元数据。按胃肠道采样位置分层的患者特征：右结肠（n=25）、左结肠（n=17）与直肠（n=18）。数据以均值（标准差）或中位数（Q1-Q3）呈现（非正态分布数据，另有说明者除外）。缺失数据以方括号标注。百分比基于有效数据计算。a：右结肠组与直肠组间P=0.038。