Deep Sequencing of the Vaginal Microbiota of Women with HIV

Ruben Hummelen,Jean M Macklaim,Gregory B Gloor,Andrew D Fernandes,Russell J Dickson,Gregor Reid,John Changalucha

doi:10.1371/journal.pone.0012078

Abstract

BackgroundWomen living with HIV and co-infected with bacterial vaginosis (BV) are at higher risk for transmitting HIV to a partner or newborn. It is poorly understood which bacterial communities constitute BV or the normal vaginal microbiota among this population and how the microbiota associated with BV responds to antibiotic treatment.Methods and FindingsThe vaginal microbiota of 132 HIV positive Tanzanian women, including 39 who received metronidazole treatment for BV, were profiled using Illumina to sequence the V6 region of the 16S rRNA gene. Of note, Gardnerella vaginalis and Lactobacillus iners were detected in each sample constituting core members of the vaginal microbiota. Eight major clusters were detected with relatively uniform microbiota compositions. Two clusters dominated by L. iners or L. crispatus were strongly associated with a normal microbiota. The L. crispatus dominated microbiota were associated with low pH, but when L. crispatus was not present, a large fraction of L. iners was required to predict a low pH. Four clusters were strongly associated with BV, and were dominated by Prevotella bivia, Lachnospiraceae, or a mixture of different species. Metronidazole treatment reduced the microbial diversity and perturbed the BV-associated microbiota, but rarely resulted in the establishment of a lactobacilli-dominated microbiota.ConclusionsIllumina based microbial profiling enabled high though-put analyses of microbial samples at a high phylogenetic resolution. The vaginal microbiota among women living with HIV in Sub-Saharan Africa constitutes several profiles associated with a normal microbiota or BV. Recurrence of BV frequently constitutes a different BV-associated profile than before antibiotic treatment.

Highlights

The human vaginal microbiota plays an important role in the maintenance of health of a woman, partner or newborn [1]
The vaginal microbiota among women living with HIV in Sub-Saharan Africa constitutes several profiles associated with a normal microbiota or bacterial vaginosis (BV)
We chose to sequence the V6 variable region of the 16S rRNA gene as it was adequate to resolve the majority of the expected organisms in the vaginal microbiota to the genus level [5] and provided resolution for a number of organisms in our samples to species and in some cases to strain level (Gloor et al submitted)

Summary

Introduction

The human vaginal microbiota plays an important role in the maintenance of health of a woman, partner or newborn [1]. We describe the development and utilization of a novel metagenomic approach based on Illumina sequencing to profile the vaginal microbiota. Illumina has fewer errors than 454 sequencing [3] and we hypothesized that it could provide a higher phylogenetic resolution than 454 based approaches [4]. Women living with HIV and co-infected with bacterial vaginosis (BV) are at higher risk for transmitting HIV to a partner or newborn. It is poorly understood which bacterial communities constitute BV or the normal vaginal microbiota among this population and how the microbiota associated with BV responds to antibiotic treatment

Methods

Results

Conclusion