S1 Meta Data, S2 Phylogenetic trees all representative OTUs, S3 Lists of species included in species* groups, S4 Counts of sequences condensed to 865 species/OTUs for compositional analyses, S5 Counts of sequences filtered to 96 species/OTUs for comparative analyses, S6 Counts of sequences filtered to 51 species/OTUs for comparative analyses, S9 Counts of sequences of a subset of pretreatment samples that distribute <i>Gardnerella</i> counts into groups of <i>Gardnerella</i> species.

(XLSX)