The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women

Abstract

The vaginal microbiome plays an important role in maternal and neonatal health. Imbalances in this microbiota (dysbiosis) during pregnancy are associated with negative reproductive outcomes, such as pregnancy loss and preterm birth, but the underlying mechanisms remain poorly understood. Consequently a comprehensive understanding of the baseline microbiome in healthy pregnancy is needed. We characterized the vaginal microbiomes of healthy pregnant women at 11-16 weeks of gestational age (n = 182) and compared them to those of non-pregnant women (n = 310). Profiles were created by pyrosequencing of the cpn60 universal target region. Microbiome profiles of pregnant women clustered into six Community State Types: I, II, III, IVC, IVD and V. Overall microbiome profiles could not be distinguished based on pregnancy status. However, the vaginal microbiomes of women with healthy ongoing pregnancies had lower richness and diversity, lower prevalence of Mycoplasma and Ureaplasma and higher bacterial load when compared to non-pregnant women. Lactobacillus abundance was also greater in the microbiomes of pregnant women with Lactobacillus-dominated CSTs in comparison with non-pregnant women. This study provides further information regarding characteristics of the vaginal microbiome of low-risk pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.

Figure 1

Vaginal microbial profiles of pregnant women at low risk of preterm birth. Heatmap of hierarchical clustering of Jensen-Shannon distance matrices with Ward linkage on the relative proportions of reads for each OTU within individual vaginal samples (n = 182). Each column represents a woman’s vaginal microbiome profile, and each row represents an OTU. Only OTU that are at least 1% abundant in at least one sample are shown. The proportion of the total microbiome comprised is indicated by white to red colour according to the legend. The coloured bars above the heatmap show the community state type (CST) and the Nugent score category (Nugent) for each woman. Legend: white = missing data.

Figure 2

CST and pregnancy status of participants. Jackknifed principal coordinates analysis (PCoA) of Bray-Curtis distance matrices of microbial profiles from all participants in the study, with individuals coloured by CST (A) or pregnancy status (B). Samples with fewer than 1000 sequence reads (16/492) were not plotted.

Figure 3

Lactobacillus spp. abundance. Bimodal distribution of vaginal microbiome profiles of non-pregnant (upper panel) and pregnant (lower panel) women based on Lactobacillus spp. abundance (%).

Figure 4

Comparison of the microbial community features between pregnant and non-pregnant participants within each CST. Lactobacillus spp. abundance (A), Shannon diversity (B), Chao1 richness (C), Mollicutes prevalence (D), Ureaplasma prevalence (E) and bacterial load (F) were compared between pregnant and non-pregnant women in each CST. For continuous variables (A–C,F), the mean value is plotted with error bars indicating standard deviation. Significant differences (p < 0.05) between pregnant and non-pregnant women within each CST are indicated by an asterisk. p-values in the main panels refer to the comparison between pregnant and non-pregnant women in Lactobacillus-dominated CST (yellow panel) and non-Lactobacillus-dominated CST (blue panel). A comparison of pooled data from all CST is shown in the right-most panel. Statistical tests used are indicated on the right side of the graph.

Figure 5

Socio-demographic characteristics of pregnant participants in relation to CST. Hierarchical clustering of microbiome profiles based on Jensen-Shannon distance matrices with Ward linkage of the relative proportions each OTU within individual vaginal samples (n = 182). Demographic characteristics are indicated on the left side, and categories indicated on the right side of each row. Numbers on the right side indicate adjusted p-values of Chi-square test after false discovery rate correction. Fisher’s Exact test was conducted for variables where at least one category had an expected frequency of less than 5. Legend: white = missing data.