Vaginal microbiome (VM) is dominated by Lactobacillus for maintenance of vaginal health. The objective of this study was to characterize changes in the VM during the menstrual cycle of HIV positive (HIV+) and HIV negative (HIV-) women in a sub-urban population of Kenya. In this longitudinal study of 38 women-20 HIV+,18 HIV-high vaginal swabs were for genomic DNA and Gram stain and quantitative PCR (qPCR). qPCR nested on Gram stain showed high concentration of L. iners in normal VM, increasing during bacterial vaginosis (BV) and high levels of L. jensenii in women with BV while L. crispatus was absent. G. vaginalis increased from normal to BV. A. vaginae was absent in normal but detectable in intermediate gram stain and increased during BV. Gram stain showed BV was absent in HIV-ve women using condoms. Both groups had high concentration L. iners and G. vaginalis, harboured A. vaginae. Frequency and concentration of L. crispatus were less in HIV+ women, L. jensenii undetectable but condom use significantly higher. Menstrual cycle showed high concentration of L. iners and G. vaginalis. L. crispatus increased while A. vaginae decreased. At the initial phase, L. jensenii was low and undetectable thereafter. In this Kenyan population L. iners predominates normal VM, increased during BV. Both groups had high concentration of L. iners and G. vaginalis. Concentration of L. crispatus increased while A. vaginae decreased. Condoms and L. crispatus show protection against BV while L. jensenii does not. Both the presence and quantities of L. crispatus determine healthy VM.
Key words: Vaginal microbiome, HIV, qPCR, Lactobacilli, menstrual cycle.
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