Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes

Abstract

Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the question if genetic differences among strains might distinguish potentially pathogenic from commensal strains. To disentangle the diversity of G. vaginalis, we invoked the concept of ecotypes—lineages of genetically and ecologically distinct strains within a named species—to better understand their evolutionary history and identify functional characteristics. We compared the genomes of G. vaginalis to six species in the closely related Bifidobacterium genus and found that G. vaginalis has a large accessory genome relative to Bifidobacterium, including many unique genes possibly involved in metabolism, drug resistance, and virulence. We then performed a comparative genomic analysis of 35 strains of G. vaginalis to infer a phylogeny based on the combined analysis of the core genome, using nucleotide substitution models, and the accessory genome, using gene gain/loss models. With the inferred tree topology, we performed comparisons of functional gene content among lineages that diverged at varying depths in the phylogeny and found significant differences in the representation of genes putatively involved in pathogenicity. Our functional enrichment analysis suggests that some lineages of G. vaginalis may possess enhanced pathogenic capabilities, including genes involved in mucus degradation like sialidases, while others may be commensal strains, lacking many of these pathogenic capabilities. The combined phylogenetic evidence and functional enrichment analysis allowed us to identify distinct ecotypes that have evolved in G. vaginalis as the result of the differential gene gain/loss for specific functions, including the capability to cause disease. We finally discuss how this analysis framework could be used to gain insight into the etiology of bacterial vaginosis and improve diagnosis.

A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

“…This pales in comparison to the number of non-redundant genes included in VIRGO for G. vaginalis, which surpasses 25,000 genes. Previous studies have highlighted the remarkable diversity of this species [29][30][31][32] . G. vaginalis is the only species analyzed which, as estimated by metagenome accumulation curves, did not approach saturation.…”

Interaction of Gardnerella vaginalis and Vaginolysin with the Apical versus Basolateral Face of a Three-Dimensional Model of Vaginal Epithelium

“…There is considerable genetic heterogeneity within the species (28,29). Multiple studies suggest that both commensal and BV-associated strains exist, potentially explaining why G. vaginalis is less BV specific than other BV-associated organisms (30)(31)(32)(33). It is often regarded as the keystone species for the establishment of BV for several reasons.…”

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population

“…Genetically distinct ecotypes with psychrotolerant or thermotolerant lifestyles were found in Bacillus cereus (Guinebretière et al ., ). Genomic differences were also observed between pathogenic and non‐pathogenic ecotypes of Gardnerella vaginallis (Cornejo et al ., ).…”