Whole 16S rRNA gene sequencing reveals differences in the oral microbiota of healthy individuals infected with oral HPV

To explore the oral microbiota in healthy individuals with and without oral human papillomavirus (HPV) infection and identify any features or changes in the oral microbiota associated with intermediate HPV infection. PacBio HiFi sequencing of the whole 16S rRNA gene was performed on 128 saliva samples from a previously characterized cohort (64 HPV-positive and 64 HPV-negative). Statistical analysis of alpha- and beta-diversity, as well as taxonomic composition (differential abundance testing), were used to determine differences between-subject groups. We demonstrated (1) significant differences in the abundance of Streptococcus salivarius in oral HPV-negative males; (2) males with low-risk HPV had an increased abundance of several species and (3) decreased abundance of Streptococcus salivarius and Streptococcus parasanguinis. For women, (4) oral microbiota Shannon diversity was significantly lower in HPV-positive subjects compared to HPV-negative subjects and (5) oral community structure (beta-diversity) was significantly different when stratified by HPV status. Intermediate oral HPV infection is associated with several perturbations in the abundance of some bacterial taxa in the oral microbiota, which differ between males and females. Further research is required to determine whether these changes contribute to oral carcinogenesis.