Resolution and co-occurrence patterns ofGardnerella leopoldii,Gardnerella swidsinskii,Gardnerella piotiiandGardnerella vaginaliswithin the vaginal microbiome

Abstract

BackgroundGardnerella vaginalis is a hallmark of vaginal dysbiosis, but is found in the microbiomes of women with and without vaginal symptoms. G. vaginalis encompasses diverse taxa differing in attributes that are potentially important for virulence, and there is evidence that ‘clades’ or ‘subgroups’ within the species are differentially associated with clinical outcomes. The G. vaginalis species description was recently emended, and three new species within the genus were defined (leopoldii, swidsinskii, piotii). 16S rRNA sequences for the four Gardnerella species are all >98.5% identical and no signature sequences differentiate them.ResultsWe demonstrated that Gardnerella species can be resolved using partial chaperonin-60 (cpn60) sequences, with pairwise percent identities of 87.1-97.8% among the type strains. Pairwise co-occurrence patterns of Gardnerella spp. in the vaginal microbiomes of 413 reproductive aged Canadian women were investigated, and several significant co-occurrences of species were identified. Abundance of G. vaginalis, and swidsinskii was associated with vaginal symptoms of abnormal odour and discharge.Conclusionscpn60 barcode sequencing can provide a rapid assessment of the relative abundance of Gardnerella spp. in microbiome samples, providing a powerful method of elucidating associations between these diverse organisms and clinical outcomes. Researchers should consider using cpn60 in place of 16S RNA for better resolution of these important organisms.

Slipped strand mispairing in the gene encoding sialidase NanH3 inGardnerellaspp

“…C10 was most common in VN014 and VN015, while C9 and C12 were most frequently observed in NR032 and W11, respectively. VN015 had the highest number of homopolymer variants ( piotii since these species co-exist in the same microbiome and women are usually colonized by more than one species (7,31,32).…”

“…Gardnerella spp. can form multi-species biofilms in vitro (46) and although "Gardnerella vaginalis" has been shown to participate in multispecies biofilms with other BV associated bacteria in vivo (47,48) (7,31,50,51) and may contribute to transition from eubyosis to dysbiosis and enhance colonization by other BV associated anaerobes. Phase variation in a cell surface associated sialidase enzyme might be critical for turning on or off the initial adhesion of Gardnerella to epithelial cells and thus the cascade of events following that result in the biofilm covered "clue cells" typical of BV (52).…”

Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome

“…isolated from the human vaginal microbiome [5]. Women with Gardnerella dominated vaginal microbiomes are usually colonized by multiple species, with G. vaginalis (cpn60 subgroup C), G. leopoldii and G. swidsinskii (subgroup A) being the most common and abundant [6, 7]. G. piotii (subgroup B) and strains belonging to several currently unnamed genome species (subgroup D) are less frequently detected and have not been observed to dominate the microbiome [6, 7].…”

“…Women with Gardnerella dominated vaginal microbiomes are usually colonized by multiple species, with G. vaginalis (cpn60 subgroup C), G. leopoldii and G. swidsinskii (subgroup A) being the most common and abundant [6, 7]. G. piotii (subgroup B) and strains belonging to several currently unnamed genome species (subgroup D) are less frequently detected and have not been observed to dominate the microbiome [6, 7]. In in vitro co-culture experiments, isolates from subgroups A, B and C had reduced fitness when co-cultured with isolates from other subgroups, but the growth rates of subgroup D isolates increased with increasing number of competitors [5].…”

“…suggesting that these isolates persist in the vaginal microbiome through negative frequency-dependent selection [8]. Vaginal microbiomes dominated by subgroup D, however, have not been reported [6, 7]. While this potentially an argument against negative frequency-dependent selection, another possibility is that the negative frequency-dependent selection of rare Gardnerella spp.…”