In Silico Analysis of Gardnerella Genomospecies Detected in the Setting of Bacterial Vaginosis

Abstract

BACKGROUND Gardnerella vaginalis is implicated as one of the causative agents of bacterial vaginosis, but it can also be isolated from the vagina of healthy women. Previous efforts to study G. vaginalis identified 4 to 6 clades, but average nucleotide identity analysis indicates that G. vaginalis may be multiple species. Recently, Gardnerella was determined to be 13 genomospecies, with Gardnerella piottii, Gardnerella leopoldii, and Gardnerella swidsinkii delineated as separate species. METHODS We accessed 103 publicly available genomes annotated as G. vaginalis. We performed comprehensive taxonomic and phylogenomic analysis to quantify the number of species called G. vaginalis, the similarity of their core genes, and their burden of their accessory genes. We additionally analyzed publicly available metatranscriptomic data sets of bacterial vaginosis to determine whether the newly delineated genomospecies are present, and to identify putative conserved features of Gardnerella pathogenesis. RESULTS Gardnerella could be classified into 8 to 14 genomospecies depending on the in silico classification tools used. Consensus classification identified 9 different Gardnerella genomospecies, here annotated as GS01 through GS09. The genomospecies could be readily distinguished by the phylogeny of their shared genes and burden of accessory genes. All of the new genomospecies were identified in metatranscriptomes of bacterial vaginosis. CONCLUSIONS Multiple Gardnerella genomospecies operating in isolation or in concert with one another may be responsible for bacterial vaginosis. These results have important implications for future efforts to understand the evolution of the Gardnerella genomospecies, host–pathogen interactions of the genomospecies during bacterial vaginosis, diagnostic assay development for bacterial vaginosis, and metagenomic investigations of the vaginal microbiota.

The structure and diversity of strain-level variation in vaginal bacteria

“…The four groups of G. vaginalis that we found encompass and are largely consistent with prior groups (Table S11) [4, 13–15]. However, a number of these previously defined groups correspond to strains we find to have mixed ancestry.…”

“…The four groups of G. vaginalis that we found encompass and are largely consistent with prior groups (Table S11) [4,[13][14][15].…”

“…However, assemblies may give the appearance of mixed ancestry if unknowingly generated using a mixture of two or more strains. More recent studies [4,14,15] have expanded the number of strains as well as the number of groups (Table S10). However, many of these new groups are comprised of strains our analysis indicates are of mixed ancestry.…”

“…For certain vaginal bacterial species, functional, phenotypic and genomic differences have been described among isolated strains. An example of this is the classification of G. vaginalis into distinct phylogenetic clades (groups) through genomic approaches such as gene ontology and genome-wide SNP analysis [13][14][15]. Characterization of individual strains have shown functional differences (including sialidase activity) between groups with phenotypic consequences [16][17][18][19].…”

Atopobium vaginae and Prevotella bivia Are Able to Incorporate and Influence Gene Expression in a Pre-Formed Gardnerella vaginalis Biofilm

“…G. vaginalis was the only recognized species in its genus for over four decades, but very recently the Gardnerella taxonomic description was amended based on comparisons of whole-genome sequencing and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry analysis, resulting in four species ( G. vaginalis , G. leopoldii , G. swidsinskii , and G. piotii ) and nine ‘genome species’ [ 15 ]. It is likely that each named Gardnerella species and ‘genome species’ are specifically associated with either BV or healthy vaginal microbiota due to differences in their virulence potential, as suggested by several studies [ 16 , 17 , 18 , 19 , 20 , 21 ]. Following this renewed taxonomy of the genus Gardnerella , in this article, the term Gardnerella spp.…”