Microbiome analysis in individuals with human papillomavirus oral infection

Microbiome gained attention as a cofactor in cancers originating from epithelial tissues. High-risk (hr)HPV infection causes oropharyngeal squamous cell carcinoma but only in a fraction of hrHPV+ individuals, suggesting that other factors play a role in cancer development. We investigated oral microbiome in cancer-free subjects harboring hrHPV oral infection (n = 33) and matched HPV- controls (n = 30). DNA purified from oral rinse-and-gargles of HIV-infected (HIV+) and HIV-uninfected (HIV-) individuals were used for 16S rRNA gene V3-V4 region amplification and sequencing. Analysis of differential microbial abundance and differential pathway abundance was performed, separately for HIV+ and HIV- individuals. Significant differences in alpha (Chao-1 and Shannon indices) and beta diversity (unweighted UniFrac distance) were observed between hrHPV+ and HPV-negative subjects, but only for the HIV- individuals. Infection by hrHPVs was associated with significant changes in the abundance of Saccharibacteria in HIV+ and Gracilibacteria in HIV- subjects. At the genus level, the greatest change in HIV+ individuals was observed for Bulleidia, which was significantly enriched in hrHPV+ subjects. In HIV- individuals, those hrHPV+ showed a significant enrichment of Parvimonas and depletion of Alloscardovia. Our data suggest a possible interplay between hrHPV infection and oral microbiome, which may vary with the HIV status.