Additional file 2 of Cataloging the phylogenetic diversity of human bladder bacterial isolates

Additional file 2: Table S1. Metadata for bladder-specific isolated genomes and hosts information. Table S2. Relative abundances of different genera in 16S sequencing samples. Table S3. Relative abundances (100%) of different GTDB-classified bacterial taxonomy in 34 metagenomics sequencing samples. Table S4. List of GTDB classified species isolated from gut, vaginal, and bladder samples. A single genome was selected for each species from the gut, vaginal, and bladder strains. Table S5. KEGG functions of bladder, gut, and vaginal genomes. Table S6. COG20 functions of bladder, gut, and vaginal genomes. Table S7. Statistical analyses of KO modules in bladder, vaginal, and gut genomes. KO module enrichment table was generated using anvi’o v7. Table S8. Statistical analyses of KOfam hits in bladder, vaginal, and gut genomes. KOfam enrichment table was generated using anvi’o v7. Table S9. Statistical analyses of COG20 functions in bladder, vaginal, and gut genomes. COG20 function enrichment table was generated using anvi’o v7. Table S10. Phylogroup distribution of bladder and gut E. coli strains. Table S11. KOfam profiles of bladder E. coli strains. Table S12. KOfam profiles of gut E. coli strains. Table S13. Differentially abundant KOfam profiles between bladder and gut E. coli isolates by Wilcoxon rank sum test. Table S14. Virulence factor genes identified in bladder E. coli isolate assemblies. Number listed is number of copies of the gene. Table S15. Antibiotic resistance genes identified in bladder E. coli isolate assemblies. Number listed is number of copies of the gene. Table S16. Virulence factor genes identified in gut E. coli isolate assemblies. Number listed is number of copies of the gene. Table S17. Antibiotic resistance genes identified in gut E. coli isolate assemblies. Number listed is number of copies of the gene. Table S18. Differentially abundant virulence and antibiotic resistance genes between bladder and gut E. coli isolates by Wilcoxon rank sum test.

附加文件2：表S1：膀胱特异性分离基因组及其宿主信息元数据。表S2：16S测序样本中不同菌属的相对丰度表。表S3：34个宏基因组测序样本中经基因组分类数据库（Genome Taxonomy Database, GTDB）分类的不同细菌分类单元的相对丰度（100%）表。表S4：从肠道、阴道及膀胱样本中分离得到的经GTDB分类的物种列表，其中从肠道、阴道和膀胱菌株的每个物种中挑选单份基因组。表S5：膀胱、肠道与阴道基因组的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）功能注释表。表S6：膀胱、肠道与阴道基因组的COG20功能注释表。表S7：膀胱、阴道与肠道基因组的KO模块统计分析表，KO模块富集表使用anvi’o v7软件生成。表S8：膀胱、阴道与肠道基因组的KOfam命中结果统计分析表，KOfam富集表使用anvi’o v7软件生成。表S9：膀胱、阴道与肠道基因组的COG20功能统计分析表，COG20功能富集表使用anvi’o v7软件生成。表S10：膀胱与肠道大肠杆菌（Escherichia coli, E. coli）菌株的系统发育群分布表。表S11：膀胱源大肠杆菌菌株的KOfam特征谱表。表S12：肠道源大肠杆菌菌株的KOfam特征谱表。表S13：通过Wilcoxon秩和检验得到的膀胱与肠道源大肠杆菌分离株间差异富集的KOfam特征谱表。表S14：膀胱源大肠杆菌分离株组装序列中鉴定到的毒力因子基因表，所列数值为对应基因的拷贝数。表S15：膀胱源大肠杆菌分离株组装序列中鉴定到的抗生素抗性基因表，所列数值为对应基因的拷贝数。表S16：肠道源大肠杆菌分离株组装序列中鉴定到的毒力因子基因表，所列数值为对应基因的拷贝数。表S17：肠道源大肠杆菌分离株组装序列中鉴定到的抗生素抗性基因表，所列数值为对应基因的拷贝数。表S18：通过Wilcoxon秩和检验得到的膀胱与肠道源大肠杆菌分离株间差异富集的毒力因子与抗生素抗性基因表。