Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis

Abstract

Background: Although the significance of the human vaginal microbiome for health and disease is increasingly acknowledged, there is paucity of data on the differences in the composition of the vaginal microbiome upon infection with different sexually transmitted pathogens.

Method: The composition of the vaginal bacterial community of women with Trichomonas vaginalis (TV, N = 18) was compared to that of women with Chlamydia trachomatis (CT, N = 14), and to that of controls (N = 21) (women negative for TV, CT and bacterial vaginosis). The vaginal bacterial composition was determined using high throughput sequencing with the Ion 16S metagenomics kit of the variable regions 2, 4 and 8 of the bacterial 16S ribosomal RNA gene from the vaginal swab DNA extract of the women. QIIME and R package "Phyloseq" were used to assess the α- and β-diversity and absolute abundance of the 16S rRNA gene per sample in the three groups. Differences in taxa at various levels were determined using the independent T-test.

Results: A total of 545 operational taxonomic units (OTUs) were identified in all the three groups of which 488 occurred in all three groups (core OTUs). Bacterial α-diversity, by both Simpson's and Shannon's indices, was significantly higher, (p = 0.056) and (p = 0.001) respectively, among women with either TV or CT than among controls (mean α-diversity TV-infected > CT-infected > Controls). At the genus level, women infected with TV had a significantly (p < 0.01) higher abundance of Parvimonas and Prevotella species compared to both controls and CT-infected women, whereas women infected with CT had a significantly (p < 0.05) higher abundance of Anaerococcus, Collinsella, Corynebacterium and Dialister.

Conclusion: The vaginal microbiomes of TV and CT-infected women were markedly different from each other and from women without TV and CT. Future studies should determine whether the altered microbiomes are merely markers of disease, or whether they actively contribute to the pathology of the two genital infections.

Fig 1. Venn diagram of the dominant OTU’s for each group.

Numbers indicate the number of operational taxonomic units OTU’s.

Fig 2. Bacterial α-diversity among the different groups of pregnant women in Kilifi, Kenya.

Dot plots represent (A) Shannon index and (B) Simpson index. Statistical analysis was performed using ANOVA. Lines inside dot plots represent mean ± standard error.

Fig 3. β-diversity of vaginal microbiomes among the different groups of pregnant women.

β-diversity of vaginal microbiomes among pregnant women with T. vaginalis (n = 18), C. trachomatis (n = 14) and the control group (n = 21). (A) Non-metric multidimensional scaling (NMDS) plot of the vaginal bacteria of the three groups. Points represent the vaginal microbiomes of individual women at all taxonomic levels; colors indicate the infection status. (B) Principle coordinates analysis (PCoA) based on Bray Curtis metrics on Operational Taxonomic Units (OTUs).

Fig 4. Bar graphs showing relative abundance of genera.

The bar graphs are of genera that were significantly different among the three groups. Women with CT and TV had more Collinsella, Dialister and Prevotella than controls. Women with CT had more Anaerococcus and Corynebacterium than women with TV. Women with TV have more Parvimonas than controls. Pair-wise comparisons are done by t-test and annotated as *; p < 0.05, **; p < 0.01. Standard error is depicted by error bars.