Background. Whether human immunodeficiency virus (HIV) infection is associated with a change in the diversity of genital microbiota in women was investigated.

Methods. Amplicon length heterogeneity polymerase chain reaction (LH-PCR) analysis and pyrosequencing of the 16S ribosomal RNA gene were used to analyze the diversity of the microbiota in HIV-positive (HIV⁺) and HIV-negative (HIV^-) women with or without bacterial vaginosis (BV).

Results. LH-PCR analysis revealed significantly more microbiota diversity in BV-positive (BV⁺) women than in BV-negative (BV^-) women, but no significant difference was noted between HIV⁺ women and HIV^- women. Pyrosequencing revealed that Lactobacillus organisms constituted a median of 96% of the bacteria in BV^- women. BV⁺ women had a significantly higher number of taxa found at ⩾1% of the total genital microbiota (median, 11 taxa). Common taxa in BV⁺ women were Prevotella, Megasphaera, Gardnerella, Coriobacterineae, Lachnospira, and Sneathia. There was a trend (P = .07) toward the presence of a higher number of taxa in HIV⁺BV⁺ women than in HIV^-BV⁺ women. Propionibacterineae, Citrobacter, and Anaerococcus were the taxa found only in HIV⁺ women (P < .05).

Conclusions. The present study demonstrated that both LH-PCR analysis and pyrosequencing differentiated microbiota in BV⁺ women from that in BV^- women and that pyrosequencing indicated a trend toward increased diversity in BV⁺HIV⁺ women, suggesting that HIV infection is associated with changes in the diversity of genital microbiota.