Vaginal microbiome of reproductive-age women

Abstract

The means by which vaginal microbiomes help prevent urogenital diseases in women and maintain health are poorly understood. To gain insight into this, the vaginal bacterial communities of 396 asymptomatic North American women who represented four ethnic groups (white, black, Hispanic, and Asian) were sampled and the species composition characterized by pyrosequencing of barcoded 16S rRNA genes. The communities clustered into five groups: four were dominated by Lactobacillus iners, L. crispatus, L. gasseri, or L. jensenii, whereas the fifth had lower proportions of lactic acid bacteria and higher proportions of strictly anaerobic organisms, indicating that a potential key ecological function, the production of lactic acid, seems to be conserved in all communities. The proportions of each community group varied among the four ethnic groups, and these differences were statistically significant [χ(2)(10) = 36.8, P < 0.0001]. Moreover, the vaginal pH of women in different ethnic groups also differed and was higher in Hispanic (pH 5.0 ± 0.59) and black (pH 4.7 ± 1.04) women as compared with Asian (pH 4.4 ± 0.59) and white (pH 4.2 ± 0.3) women. Phylotypes with correlated relative abundances were found in all communities, and these patterns were associated with either high or low Nugent scores, which are used as a factor for the diagnosis of bacterial vaginosis. The inherent differences within and between women in different ethnic groups strongly argues for a more refined definition of the kinds of bacterial communities normally found in healthy women and the need to appreciate differences between individuals so they can be taken into account in risk assessment and disease diagnosis.

Fig. 1.

Heatmap of log₁₀-transformed proportions of microbial taxa found in the vaginal bacterial communities of 394 women of reproductive age (color key is indicated in the lower right corner). (A) Complete linkage clustering of samples based on the species composition and abundance of vaginal bacterial communities that define community groups I to V. (B) Nugent scores and pH measurements for each of the 394 community samples (color key is indicated above C). (C) Complete linkage clustering of taxa based on Spearman's correlation coefficient profiles, which were defined as the set of Spearman's correlation coefficients calculated between one taxon and all of the other taxa (SI Materials and Methods). (D) Spearman's correlation coefficients between the presence of a taxon and the Nugent score or pH of a sample. (E) Shannon diversity indices calculated for 394 vaginal communities (two singletons were excluded).

Fig. 2.

Correlogram of 60 microbial taxa with negative or positive correlation to Nugent scores. Microbial taxa with the highest negative or positive correlation with Nugent scores were selected as described in SI Materials and Methods. The Spearman's correlation coefficients between each taxon and all other taxa were used to build the correlogram that illustrates the cooccurrence of taxa in communities. Spearman's correlation coefficients between taxa and Nugent scores are also indicated.

Fig. 3.

Representation of vaginal bacterial community groups within each ethnic group of women. The number of women from each ethnic group is in parentheses.

Fig. 4.

Relationships among vaginal bacterial communities visualized by principal component analysis in which the relative abundances are expressed as proportions of the total community and displayed in 3D space. Communities dominated by species of Lactobacillus and representing community groups I, II, III, and V are shown at each of the four outer vertices of the tetrahedron, with communities of group IV at the inner vertex and shown in the Inset. (A) Each point corresponds to a single subject and was colored according to the proportions of phylotypes in each community. (B) pH of each vaginal community shown in A. (C) Nugent score category of each vaginal community shown in A.