Hierarchic clustering of vaginal microbiome profiles by nearest-neighbor “species.” Only nearest-neighbor “species” comprising at least 1% of at least one sample are included. The color scale reflects the proportion of the total profile each “species” represented. Samples were divided into five clusters (indicated by numbers) based on average Jaccard similarities from 100 resampling runs. Colored blocks on the top indicate the menstrual phase of each sample. Mollicutes- and Ureaplasma-positive samples are indicated by black boxes below the heatmap (gray boxes indicate that the sample was not tested).