Microbiome analysis in individuals with human papillomavirus oral infection

Abstract

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.

Fig. 1

Alpha diversity of bacterial taxa in oral samples of high-risk HPV-positive (hrHPV+) and HPV-negative individuals (HPV−), grouped by HIV status. Shannon, Faith, Pielou Evenness and Chao1 metrics for each study group are shown.

Fig. 2

Beta diversity analysis of microbial communities in oral samples of high-risk HPV-positive (hrHPV+) and HPV-negative individuals (HPV−) using Principal Coordinates Analysis (PCoA) based on Jaccard dissimilarity, unweighted and weighted UniFrac distances. Plots are shown separately for (a) HIV-infected (HIV+) and (b) HIV-uninfected individuals (HIV−). Each circle represents a participant. The 95% confidence ellipse for each group is also shown.

Fig. 3

Taxonomic composition of the oral microbiome with the relative abundance of the most abundant taxa (abundance > 1%) at the phylum level. HIV+ HIV-infected subjects, HIV− HIV-uninfected subjects, hrHPV+ high-risk HPV-positive, HPV− HPV-negative.

Fig. 4

Differential abundance of oral bacterial taxa at the genus level. Taxa with a significant differential abundance between high-risk HPV-positive (hrHPV+) and HPV-negative subjects (HPV−) are indicated with an asterisk (p < 0.05). HIV+ HIV-infected individuals (teal bars), HIV− HIV-uninfected individuals (red bars), p phylum, c class, o order, f family, g genus, logFC log2 Fold Change.

Fig. 5

Differential pathway abundance predicted in terms of KEGG Orthology (KO) abundances. High-risk HPV-positive (hrHPV+) and HPV-negative individuals (HPV−) were compared. KO abundances with a p < 0.005 and a p < 0.01 are shown for (a) HIV-infected (HIV+) and (b) HIV-uninfected individuals (HIV−), respectively. LogFC log2 Fold Change.