Additional file 3 of Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer

Additional file 2: Supplemental Table 1. Summary information for genes discussed in this study including abbreviations, full gene name, reaction the gene catalyzes, and HMM information. Supplemental Table 2. Summary table of HMM results where “gene” indicates that gene was found in the MAG and “N/A” indicates the gene was not found in the MAG. Supplemental Table 3. Summary values of participants and MAGs with and without sulfur genes. These data were used to generate dot plots. Supplemental Table 4. Summary of MAG genera and gene hits associated with each genera from the study in addition to any previous associations of that genera with colorectal cancer and production of H2S. Supplemental Table 5. MAGs associated with complete and partial taurine pathways. Supplemental Table 6. Results from chi squared tests for associations of gene presence with participant disease status. Both uncorrected and corrected p-values are reported. Supplemental Table 7. Results from ANOVA tests for associations between presence and absence of sulfur genes and stage of colorectal cancer. Both uncorrected and corrected p-values are reported. Supplemental Table 8. Growth rate values generated by iRep for indicator species of colorectal cancer for 4 of the 5 studies used in our work. Supplemental Table 9. Results from Kruskal Wallis analysis for differences in growth rates for the aggregate data for CRC versus healthy and each individual study including comparisons across CRC, healthy, and adenoma, if present. Supplemental Table 10. Summary of taxonomy of MAGs including classification from original paper constructing MAGs (assigned and closest designators), SILVA classification based on 16S rRNA sequences, and GTDB-tk classifications.

附加文件2：补充表1。本研究讨论的基因的汇总信息，包含缩写、基因全称、该基因所催化的反应，以及隐马尔可夫模型（Hidden Markov Model，HMM）相关信息。
补充表2。隐马尔可夫模型（Hidden Markov Model，HMM）结果汇总表，其中“gene”表示该基因在宏基因组组装基因组（Metagenome-Assembled Genome，MAG）中被检出，“N/A”表示该基因未在MAG中被检出。
补充表3。携带与未携带硫代谢基因的受试者及宏基因组组装基因组（MAG）的汇总数据，此类数据用于生成散点图。
补充表4。本研究中各属水平宏基因组组装基因组（MAG）及其相关基因命中情况的汇总，此外还包含该属与结直肠癌（Colorectal Cancer，CRC）及硫化氢（Hydrogen Sulfide，H₂S）生成相关的既往研究关联。
补充表5。与完整及部分牛磺酸代谢通路相关的宏基因组组装基因组（MAG）。
补充表6。卡方检验（Chi-squared test）结果，用于分析基因存在与否与受试者疾病状态之间的关联，报告未校正与校正后的P值。
补充表7。方差分析（Analysis of Variance，ANOVA）结果，用于分析硫代谢基因的存在/缺失与结直肠癌（CRC）分期之间的关联，报告未校正与校正后的P值。
补充表8。本研究使用的5项研究中的4项，通过iRep工具计算得到的结直肠癌（CRC）指示物种的生长速率数值。
补充表9。Kruskal-Wallis检验结果，用于分析结直肠癌（CRC）患者与健康受试者的汇总数据生长速率差异，以及各单项研究（若存在则涵盖CRC、健康受试者及腺瘤组的比较）的生长速率差异。
补充表10。宏基因组组装基因组（MAG）的分类学汇总信息，包括构建MAG的原始论文中的分类结果（已分配的分类单元及最相近的分类标识）、基于16S rRNA序列的SILVA分类结果，以及GTDB-tk分类结果。