Pregnancy's stronghold on the vaginal microbiome - PubMed (original) (raw)

Pregnancy's stronghold on the vaginal microbiome

Marina R S Walther-António et al. PLoS One. 2014.

Abstract

Objective: To assess the vaginal microbiome throughout full-term uncomplicated pregnancy.

Methods: Vaginal swabs were obtained from twelve pregnant women at 8-week intervals throughout their uncomplicated pregnancies. Patients with symptoms of vaginal infection or with recent antibiotic use were excluded. Swabs were obtained from the posterior fornix and cervix at 8-12, 17-21, 27-31, and 36-38 weeks of gestation. The microbial community was profiled using hypervariable tag sequencing of the V3-V5 region of the 16S rRNA gene, producing approximately 8 million reads on the Illumina MiSeq.

Results: Samples were dominated by a single genus, Lactobacillus, and exhibited low species diversity. For a majority of the patients (n = 8), the vaginal microbiome was dominated by Lactobacillus crispatus throughout pregnancy. Two patients showed Lactobacillus iners dominance during the course of pregnancy, and two showed a shift between the first and second trimester from L. crispatus to L. iners dominance. In all of the samples only these two species were identified, and were found at an abundance of higher than 1% in this study. Comparative analyses also showed that the vaginal microbiome during pregnancy is characterized by a marked dominance of Lactobacillus species in both Caucasian and African-American subjects. In addition, our Caucasian subject population clustered by trimester and progressed towards a common attractor while African-American women clustered by subject instead and did not progress towards a common attractor.

Conclusion: Our analyses indicate normal pregnancy is characterized by a microbiome that has low diversity and high stability. While Lactobacillus species strongly dominate the vaginal environment during pregnancy across the two studied ethnicities, observed differences between the longitudinal dynamics of the analyzed populations may contribute to divergent risk for pregnancy complications. This helps establish a baseline for investigating the role of the microbiome in complications of pregnancy such as preterm labor and preterm delivery.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Pie charts representing the bacterial distribution found in each of the samples represented.

Subject 101 is representative of 7 other patients with similar profiles (Subjects 104, 105, 106, 107, 109, 113 and 114). Subject 103 and Subject 110 have similar profiles. Subject 108 and Subject 111 have similar profiles. Divisions within the pie charts represent different OTUs (Operational Taxonomic Units – Strain level). “Other” represents OTUs with ≤1% abundance that belong to various species, excluding L. crispatus and L. iners.

Figure 2

Figure 2. Principal Component Analysis (PCA) of temporal dynamics of the vaginal microbiome during pregnancy.

Arrows indicate shifts from the first timepoint, taken at 8–12 weeks, and the subsequent timepoints. Notice that all temporal profiles that involve L. iners dominance involve a shift in the microbiome profile while purely L. crispatus dominated temporal profiles do not. Visualization carried out using Matplotlib version 1.2.1 (The MathWorks, Inc.).

Figure 3

Figure 3. Shannon Diversity Index for the vaginal microbiome samples.

The profile characterized by a dominance of L. crispatus throughout pregnancy (shared by 8 of the subjects) is significantly less diverse than the two other profiles (except during the first trimester). * p<0.05; ** p<0.005 on paired t-test.

Figure 4

Figure 4. Pregnancy effect in African-American and Caucasian subjects as measured by Chao1 diversity Index.

Diversity is significantly reduced during pregnancy in both ethnicities (**p<0.01, Monte Carlo analyses, 999 permutations).

Figure 5

Figure 5. Unweighted Unifrac beta-diversity between pregnant and non-pregnant subjects within each ethnicity.

Caucasians show significant convergence as a result of pregnancy (results confounded by platform effects – See Table S1) while African-Americans show significant divergence in pregnancy when compared to non-pregnant subjects. **p<0.001, Monte Carlo analyses, 999 permutations.

Figure 6

Figure 6. Lactobacillus species frequencies across ethnicities and pregnancy states.

Significant differences were found between all categories except between pregnant Caucasians and pregnant African-Americans (*p<0.05;**p<0.01; Monte Carlo analysis, 999 permutations).

Figure 7

Figure 7. Estimation of species richness according to Chao 1 index.

A – African-American subjects (Red – N009, Orange – N018, Blue – N017). Diversity between subjects is significant and therefore does not allow for the grouping of the subjects for analytical purposes. B – Caucasian subjects. No significant differences in diversity were found among subjects.

Figure 8

Figure 8. Unweighted PCA analysis by Subject and Trimester.

A – African-American by Subject. Clustering by Subject can be observed. B – Caucasian by Subject. No clear clustering is observed. C – African-American by Trimester. No common attractor can be identified. D – Caucasian by Trimester. A common attractor can be observed. Plots C and D – 1st Trimester – Red; 2nd Trimester – Blue; 3rd Trimester – Orange.

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