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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).    Discussion  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.

Comparison of Lower Genital Tract Microbiota in HIV-Infected and Uninfected Women from Rwanda and the US