Additional file 2 of Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes

Additional file 2: Supplementary Table S1. Full ASV table for samples sequenced by 16S marker gene sequencing. Each sample is in a column, named by individual ID and cycle day, and each ASV in a row. Taxonomic annotations are in the second-to-last column and centroid sequence in the last. Supplementary Table S2. Full taxonomic annotation and feature counts for the samples sequenced by shotgun. Each sample is in a column, named by participant and cycle day, and each taxon in a row. Supplementary Table S3. Differential abundance results for samples in CST-IA from individuals with menses-related dysbiotic or unstable VCD compared to constant eubiotic VCD. Supplementary Table S4. Differential abundance results for samples in CST-IB from individuals with menses-related dysbiotic or unstable VCD compared to constant eubiotic VCD. Supplementary Table S5. Differential abundance results for samples in CST-IIIA from individuals with menses-related dysbiotic or unstable VCD compared to constant dysbiotic VCD. Supplementary Table S6. Differential abundance results for samples in CST-IIIB from individuals with menses-related dysbiotic or unstable VCD compared to constant dysbiotic VCD. Supplementary Table S7. Differential abundance results for all samples in menses-related dysbiotic, unstable and constant dysbiotic VCD against constant eubiotic. Supplementary Table S8. Differential abundance results for all samples in menses-related dysbiotic, unstable and constant eubiotic VCD against constant dysbiotic. Supplementary Table S9. Differential frequency of gene clusters in Lactobacillus spp., contrasting constant eubiotic and menses-related dysbiotic vs. unstable and constant dysbiotic. Supplementary Table S10. Differential frequency of gene clusters in Gardnerella spp., contrasting constant eubiotic and menses-related dysbiotic vs. unstable and constant dysbiotic. Supplementary Table S11. Differential frequency of gene clusters in Prevotella spp., contrasting constant eubiotic and menses-related eubiotic vs. unstable and constant dysbiotic.

附加文件2：补充表S1。本文件为通过16S标记基因测序得到的样本的完整扩增子序列变异（Amplicon Sequence Variant, ASV）表：以列表示单个样本，样本命名格式为「个体ID+周期天数」；以行表示单个ASV。表格倒数第二列为分类学注释信息，最后一列为中心序列。补充表S2。本文件为通过鸟枪测序得到的样本的完整分类学注释与特征计数表：以列表示单个样本，样本命名格式为「受试者ID+周期天数」；以行表示单个分类单元。补充表S3。本文件包含CST-IA分组样本的差异丰度分析结果，以持续共生型VCD为对照，分析对象为存在月经相关失调型或不稳定型VCD的个体。补充表S4。本文件包含CST-IB分组样本的差异丰度分析结果，以持续共生型VCD为对照，分析对象为存在月经相关失调型或不稳定型VCD的个体。补充表S5。本文件包含CST-IIIA分组样本的差异丰度分析结果，以持续失调型VCD为对照，分析对象为存在月经相关失调型或不稳定型VCD的个体。补充表S6。本文件包含CST-IIIB分组样本的差异丰度分析结果，以持续失调型VCD为对照，分析对象为存在月经相关失调型或不稳定型VCD的个体。补充表S7。本文件包含所有属于月经相关失调型、不稳定型与持续失调型VCD的样本的差异丰度分析结果，以持续共生型VCD为对照。补充表S8。本文件包含所有属于月经相关失调型、不稳定型与持续共生型VCD的样本的差异丰度分析结果，以持续失调型VCD为对照。补充表S9。本文件包含乳杆菌属（*Lactobacillus* spp.）的基因簇差异频率分析结果，对比组别为「持续共生型VCD与月经相关失调型VCD」与「不稳定型VCD与持续失调型VCD」。补充表S10。本文件包含加德纳菌属（*Gardnerella* spp.）的基因簇差异频率分析结果，对比组别为「持续共生型VCD与月经相关失调型VCD」与「不稳定型VCD与持续失调型VCD」。补充表S11。本文件包含普雷沃菌属（*Prevotella* spp.）的基因簇差异频率分析结果，对比组别为「持续共生型VCD与月经相关共生型VCD」与「不稳定型VCD与持续失调型VCD」。