AbstractThe vaginal microbiome has been linked to numerous negative health outcomes including preterm birth. Specific taxa, includingGardnerellaspp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated allGardnerellaspp. as one species, but the broad diversity ofGardnerellahas recently become more apparent. In the present study, we explore the diversity ofGardnerellaclades and genomic species in the vaginal microbiome of pregnant women and their impacts on microbiome composition and associations with preterm birth.Shotgun metagenomic sequencing data collected longitudinally from three distinct cohorts of pregnant women were assessed. Relative abundance ofGardnerellaclades and genomic species and other taxa was quantified, and associations betweenGardnerellaclades and signatures of the vaginal microbiome were measured. We also assessed the diversity and abundance ofGardnerellavariants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations on the vaginal microbiome and preterm birth.Individual microbiomes often contained multipleGardnerellavariants, and the number of clades was associated with increased microbial load. The genusGardnerellawas also associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns matched previously described community structures, and were largely consistent acrossGardnerellaclades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity ofGardnerella.The diversity ofGardnerellaboth across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome.1The broad genomic diversity ofGardnerellahas led to its reclassification as multiple species; here we demonstrate the diversity ofGardnerellafound within and between vaginal microbiomes. Further studies should investigate the phenotypes ofGardnerellavariants that may underlie the mechanisms by whichGardnerellaspecies may differentially shape the vaginal microbiome.