Comparative Abundance and Functional Biomarkers of the Vaginal and Gut Microbiome of Nigerian Women with Bacterial Vaginosis: A Study with 16S rRNA Metagenomics

Abstract

<strong>ABSTRACT</strong><br> <strong>Introduction</strong>: There are no molecular data regarding the composition of the vagina and gut microbiome of<br> Nigerian women with bacterial vaginosis (BV), mostly due to lack of appropriate application of high throughput<br> sequencing methods. Here, we aimed to characterize and compare the vaginal and gut microbiome of women with<br> bacterial vaginosis.<br> <strong>Material and Methods</strong>: Bacterial vaginosis was initially diagnosed using the Nugent scoring method among 220<br> women aged 18 to 45 years. Five BV positive samples (vagina and gut) were randomly selected and sequenced<br> with Illumina MiSeq platform for the 16S rRNA V4 region using custom-barcoded primers. Alpha-diversity was<br> estimated for species richness by ACE, Chao1 and Jackknife method, while the diversity index was calculated by<br> Shannon, Non-parametric Shannon, and Simpson index. For beta-diversity, Jensen-Shannon metrics were used<br> for principle coordinates (2D) analysis at the species level.<br> <strong>Results</strong>: Nugent scoring method showed 43 (19.5%) of the subjects had BV. The Shannon diversity index for<br> vagina and gut samples for Subject 1, 2, 3, 4 and 5 was 2.51/3.76, 1.96/3.18, 0.28/4.69, 1.67/3.14, 1.58/3.94<br> respectively. The average distribution of phyla, class, order, family, genera, and species in the vaginal microbiome<br> was 9.4, 16.8, 31.2, 63.8, 109 and 161.4 respectively whereas, in gut microbiome it was 19.6, 34.2, 68.8, 136.2,<br> 274.4, and 410.8 respectively. Relative abundance showed <em>Firmicutes</em> followed by <em>Actinobacteria</em>,<br> <em>Proteobacteria</em>, dominated the vagina while gut microbiome was dominated by <em>Firmicutes</em> followed by<br> <em>Bacteroidetes</em>, and <em>Proteobacteria</em>. The phylogenetic diversity of the vagina was significantly lower than that of<br> the gut. However, 12 genera out of 20 associated with BV were recovered from both niches with different<br> abundance among the subjects. Functional prediction using PICRUSt and LEfSe revealed significant differences<br> between the vagina and gut microbiome in the relative abundance of microbial genes related to some metabolic<br> pathways.<br> Conclusion: This is the first study using metagenomics in Nigeria that has provided an insight into the<br> phylogenetic diversity and species richness of the vagina and gut microbiome of reproductive age women with<br> BV. In addition, the study revealed relative abundances of microbial genes associated with metabolic functions<br> that are upregulated in the vagina and gut of BV subjects.