Additional file 1 of Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes
Creators: name: Hugerth, Luisa W.
name: Krog, Maria Christine
name: Vomstein, Kilian
name: Du, Juan
name: Bashir, Zahra
name: Kaldhusdal, Vilde
name: Fransson, Emma
name: Engstrand, Lars
name: Nielsen, Henriette Svarre
name: Schuppe-Koistinen, Ina
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: Biotechnology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Supplementary Figure S1. Bacterial and viral profiles for each sample over one menstrual cycle. Each participant’s bacterial and viral profile are depicted as area plots. Sexual intercourse is overlaid as blue dots and vaginal bleedings as red dots. Log10 of the ratio of viral to bacterial reads is shown as a black line over the viral profiles, for time-series with sufficient data (&gt; 5 samples with detectable phages). Missing data is omitted. Next to each taxonomic profile is an ordination showing all samples in the study as gray circles, and the samples for the relevant participant as numbers, following the days of their menstrual cycle. Days with vaginal bleedings are shown in red, days with sexual intercourse in blue and days with both events in purple. Supplementary Figure S2. CST distribution and time-series dynamics for the 16S samples. CSTs are shown as colored dots as per the legend in the second part. The outline of each box depicts the assignment to vaginal community dynamics. Missing samples are omitted. Bleedings are marked as red dots. Blue: constant eubiotic. Green: menses-related dysbiotic. Yellow: unstable. Red: constant dysbiotic. Supplementary Figure S3. CST distribution and time-series dynamics for the shotgun samples. CSTs are marked as colored dots above the taxonomic profiles as per the legend. The outline of each box depicts its dynamic group. Bleedings are marked as light red dots. Missing samples are omitted. Blue: constant eubiotic. Green: menses-related dysbiotic. Yellow: Unstable. Red: constant dysbiotic. Supplementary Figure S4. Log-fold change of bacterial species in samples from CST-I. Samples in CST-IA and CST-IB from menses-related dysbiotic or unstable individuals were compared to constant eubiotic individuals. The heatmap shows the log-fold change of all significant differences. Gray fields represent no significant change. Supplementary Figure S5. Log-fold change of bacterial species in samples from CST-III. Samples in CST-IIIA and CST-IIIB from menses-related dysbiotic or unstable individuals were compared with constant dysbiotic individuals. The heatmap shows the log-fold change of all significant differences. White fields represent no significant change. Supplementary Figure S6. Volcano plots for the vaginal community dynamics compared to either constant eubiotic or constant dysbiotic. Supplementary Figure S7. Histograms showing gene cluster prevalence in nine relevant pangenomes. For each species, the prevalence (number of genomes containing each gene cluster) of each gene cluster is shown as a histogram. Gene clusters present in most or all genomes are considered “core”, while those in one or very few genomes can be considered “cloud”. The “shell” genomes, present in many, but not all genomes, are less frequent in this dataset. Supplementary Figure S8. Phylogenomic analysis of Lactobacillus genomes. Phylogenomic analysis of all detected Lactobacillus species does not find a correlation between the womens’ vaginal community dynamics and the observed phylogeny. The presence of a gene is represented in dark blue and its absence in light blue. Blue: constant eubiotic. Red: constant dysbiotic. Yellow: unstable. Green: menses-related dysbiotic. Supplementary Figure S9. Phylogenomic analysis of Prevotella genomes. Phylogenomic analysis of all detected Prevotella species does not find a correlation between the womens’ vaginal community dynamics and the observed phylogeny. The presence of a gene is represented in dark blue and its absence in light blue. Blue: constant eubiotic. Red: constant dysbiotic. Yellow: unstable. Green: menses-related dysbiotic.