Our results demonstrate that the cpn60 universal target sequence differentiates distinct subgroups within G. vaginalis and that only one of these subgroups (Subgroup B: Piot biotype 5, sialidase positive and ARDRA genotype 1) was found to be significantly more abundant in women with BV (high Nugent score) than women with normal vaginal microbiota in a retrospective analysis of metagenomic profiles of Kenyan women. This evidence concerns the gene HSPD1 and bacterial vaginosis.