title: Deep sequencing of the vaginal microbiota of women with HIV.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  Illumina 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.
authors: Canadian Research & Development Centre for Probiotics, Lawson Health Research Institute, London, Canada.
authors: Ruben
authors: R
authors: Hummelen
authors: Andrew D
authors: AD
authors: Fernandes
authors: Jean M
authors: JM
authors: Macklaim
authors: Russell J
authors: RJ
authors: Dickson
authors: John
authors: J
authors: Changalucha
authors: Gregory B
authors: GB
authors: Gloor
authors: Gregor
authors: G
authors: Reid
mesh_terms: D000293:Adolescent; D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D005260:Female; D006194:Gardnerella vaginalis / Q000187:drug effects / Q000235:genetics; D015658:HIV Infections / Q000150:complications / Q000382:microbiology*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007778:Lactobacillus / Q000187:drug effects / Q000235:genetics; D054892:Metagenome / Q000187:drug effects / Q000235:genetics*; D008795:Metronidazole / Q000494:pharmacology; D008875:Middle Aged; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014621:Vagina / Q000737:chemistry / Q000382:microbiology*; D016585:Vaginosis, Bacterial / Q000150:complications / Q000175:diagnosis / Q000382:microbiology; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D008795:Metronidazole