The vaginal microbiome during pregnancy and the postpartum period in a European population

Abstract

The composition and structure of the pregnancy vaginal microbiome may influence susceptibility to adverse pregnancy outcomes. Studies on the pregnant vaginal microbiome have largely been limited to Northern American populations. Using MiSeq sequencing of 16S rRNA gene amplicons, we characterised the vaginal microbiota of a mixed British cohort of women (n = 42) who experienced uncomplicated term delivery and who were sampled longitudinally throughout pregnancy (8-12, 20-22, 28-30 and 34-36 weeks gestation) and 6 weeks postpartum. We show that vaginal microbiome composition dramatically changes postpartum to become less Lactobacillus spp. dominant with increased alpha-diversity irrespective of the community structure during pregnancy and independent of ethnicity. While the pregnancy vaginal microbiome was characteristically dominated by Lactobacillus spp. and low alpha-diversity, unlike Northern American populations, a significant number of pregnant women this British population had a L. jensenii-dominated microbiome characterised by low alpha-diversity. L. jensenii was predominantly observed in women of Asian and Caucasian ethnicity whereas L. gasseri was absent in samples from Black women. This study reveals new insights into biogeographical and ethnic effects upon the pregnancy and postpartum vaginal microbiome and has important implications for future studies exploring relationships between the vaginal microbiome, host health and pregnancy outcomes.

Figure 1. Bacterial class diversity is significantly increased postpartum.

(A) Principal component analysis of the vaginal bacterial classes during gestation and 6 weeks postpartum shows that post pregnancy is associated with a marked shift in the microbiome in a high proportion of sampled women. The majority of relative bacterial class abundance variation in the data set was described by the first two principal components (PC; PC1 = 92%, PC2 = 6.4%). (B) Lowest diversity was observed in samples collected from women mid-gestation with a significant increase diversity seen between 32–36 weeks gestation. A significant increase in diversity was observed postpartum determined by ANOVA with Tukey-Kramer post hoc test using a Benjamini-Hochberg FDR correction. Data is presented at mean proportions of total sequence data (left side) and differences in mean proportions (right side) compared to postpartum samples. (C) The vaginal microbiome postpartum is characterised by a significant decrease in the Bacilli class of bacteria as well as proportional increased in Clostridia, Bacteroidia and Actinobacteria classes. (D) The postpartum period was also associated with increased richness as determined by the average number of species observed and (E) as a function of sequence depth as assessed using a rarefraction curve.

Figure 2. Bacterial species composition of vaginal community state types (CST) throughout pregnancy and postpartum.

(A) Hierarchical clustering analysis using centroid linkage of microbial species data shows that vaginal microbiomes from a UK cohort can be clustered into 5 major groups consistent with vaginal CSTs previously identified in non-pregnant and pregnant North American populations. Around 75% of all postpartum samples were found to cluster into CST-IV. (B) Heatmap of relative abundances of bacterial species characterising the CSTs. (C&D) CSTs I, III and IV were represented by similar proportions of White, Asian and Black ethnicities however CST II and V were almost void of representation from black women. CST * indicates Lactobacillus amylovorous dominated microbiome.

Figure 3. Vaginal community state types (CST) throughout pregnancy and postpartum in a UK population.

(A) Longitudinal samples were assigned to CSTs on the basis of ward linkage clustering of microbial species data (CST I, red; CST II, green; CST III, orange, CST IV, blue and CST V, yellow. CST * indicates Lactobacillus amylovorous dominated microbiome). Corresponding inverse Simpson indices are presented adjacent (white indicates low diversity, dark blue indicates high diversity). (B) Samples from CST I displayed the lowest diversity as measured by the mean inverse Simpson index whereas CST IV showed significantly higher diversity. No difference in diversity was observed between CST I and CST V. (C) CST IV was associated with increased richness as described by number of species observed. ***P < 0.001, **P < 0.01, *P < 0.05. Kruskall-Wallis test (Dunn's post hoc).

Figure 4. Major microbial community structure changes in the pregnant vagina are independent of ethnicity.

(A) Principal component analysis of the vaginal microbiome class data show that high diversity or low diversity is not associated with ethnicity. (B) Levels of Lactobacillus gasseri (dominant taxa feature of CST V) are significantly less in black women compared to white women (Welch's t-test with Benjamini-Hochberg FDR correction). (C) Proportion of sequences attributed to Lactobacillus gasseri in samples derived from White, Asian and Black ethnicities clearly shows increased frequency of this species in White compared to Black.