title: Comparison of lower genital tract microbiota in HIV-infected and uninfected women from Rwanda and the US.
abstract: BACKGROUND
  Previous studies have shown that alterations of the bacterial microbiota in the lower female genital tract influence susceptibility to HIV infection and shedding. We assessed geographic differences in types of genital microbiota between HIV-infected and uninfected women from Rwanda and the United States.
  
  
  METHODS
  Genera of lower genital tract bacterial microbiota were identified by high-throughput pyrosequencing of the 16S rRNA gene from 46 US women (36 HIV-infected, 10 HIV-uninfected) and 40 Rwandan women (18 HIV-infected, 22 HIV-uninfected) with similar proportions of low (0-3) Nugent scores. Species of Lactobacillus were identified by assembling sequences along with reference sequences into phylogenetic trees. Prevalence of genera and Lactobacillus species were compared using Fisher's exact tests.
  
  
  RESULTS
  Overall the seven most prevalent genera were Lactobacillus (74%), Prevotella (56%), Gardnerella (55%), Atopobium (42%), Sneathia (37%), Megasphaera (30%), and Parvimonas (26%), observed at similar prevalences comparing Rwandan to US women, except for Megasphaera (20% vs. 39%, p = 0.06). Additionally, Rwandan women had higher frequencies of Mycoplasma (23% vs. 7%, p = 0.06) and Eggerthella (13% vs. 0%, p = 0.02), and lower frequencies of Lachnobacterium (8% vs. 35%, p<0.01) and Allisonella (5% vs. 30%, p<0.01), compared with US women. The prevalence of Mycoplasma was highest (p<0.05) in HIV-infected Rwandan women (39%), compared to HIV-infected US women (6%), HIV-uninfected Rwandan (9%) and US (10%) women. The most prevalent lactobacillus species in both Rwandan and US women was L. iners (58% vs. 76%, p = 0.11), followed by L. crispatus (28% vs. 30%, p = 0.82), L. jensenii (20% vs. 24%, p = 0.80), L. gasseri (20% vs. 11%, p = 0.37) and L. vaginalis (20% vs. 7%, p = 0.10).
  
  
  CONCLUSIONS
  We found similar prevalence of most major bacterial genera and Lactobacillus species in Rwandan and US women. Further work will be needed to establish whether observed differences differentially impact lower genital tract health or susceptibility to genital infections.
authors.affiliation: Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America.
authors.forename: Lorie
authors.initials: L
authors.lastname: Benning
authors.affiliation: Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America.
authors.forename: Elizabeth T
authors.initials: ET
authors.lastname: Golub
authors.affiliation: Departments of Medicine and Epidemiology & Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Anastos
authors.affiliation: Ruth M. Rothstein CORE Center, Stroger Hospital of Cook County, Chicago, Illinois, United States of America; Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Audrey L
authors.initials: AL
authors.lastname: French
authors.affiliation: Ruth M. Rothstein CORE Center, Stroger Hospital of Cook County, Chicago, Illinois, United States of America; Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Mardge
authors.initials: M
authors.lastname: Cohen
authors.affiliation: Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Douglas
authors.initials: D
authors.lastname: Gilbert
authors.affiliation: Department of Environmental Science and Policy, George Mason University Microbiome Analysis Center, Manassas, Virginia, United States of America.
authors.forename: Patrick
authors.initials: P
authors.lastname: Gillevet
authors.affiliation: Department of Biomedical Services, Rwanda Biomedical Center National Reference Laboratory Division, Kigali, Rwanda.
authors.forename: Elisaphane
authors.initials: E
authors.lastname: Munyazesa
authors.affiliation: Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Alan L
authors.initials: AL
authors.lastname: Landay
authors.affiliation: Department of Environmental Science and Policy, George Mason University Microbiome Analysis Center, Manassas, Virginia, United States of America.
authors.forename: Masoumeh
authors.initials: M
authors.lastname: Sikaroodi
authors.affiliation: Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Gregory T
authors.initials: GT
authors.lastname: Spear
mesh_terms: D000328:Adult; D016022:Case-Control Studies; D005260:Female; D005836:Genitalia, Female / Q000382:microbiology*; D015658:HIV Infections / Q000382:microbiology*; D018023:HIV Seronegativity; D006801:Humans; D064307:Microbiota; D008875:Middle Aged; D012432:Rwanda; D014481:United States; D016585:Vaginosis, Bacterial / Q000382:microbiology