Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth

Abstract

The vaginal microbiome has been linked to numerous negative health outcomes including preterm birth. Specific taxa, including Gardnerella spp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated all Gardnerella spp. as one species, but the broad diversity of Gardnerella has recently become more apparent. In the present study, we explore the diversity of Gardnerella clades 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 of Gardnerella clades and genomic species and other taxa was quantified, and associations between Gardnerella clades and signatures of the vaginal microbiome were measured. We also assessed the diversity and abundance of Gardnerella variants 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 multiple Gardnerella variants, and the number of clades was associated with increased microbial load. The genus Gardnerella was 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 across Gardnerella clades 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 of Gardnerella. The diversity of Gardnerella both 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.1 The broad genomic diversity of Gardnerella has led to its reclassification as multiple species; here we demonstrate the diversity of Gardnerella found within and between vaginal microbiomes. Further studies should investigate the phenotypes of Gardnerella variants that may underlie the mechanisms by which Gardnerella species may differentially shape the vaginal microbiome.