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.