Implications of Alpha and Beta Human Papillomaviruses Infection in the Oral Microbiome from Mexican Subjects Living with HIV

Human papillomavirus (HPV) infection and oral microbiota alterations have been independently associated with oral disease in people living with HIV (PLHIV). However, the relationship between alpha-HPV (α-HPV), beta-HPV (β-HPV), and the oral microbiome remains poorly understood. This cross-sectional study aimed to describe the association between oral HPV infection and the oral and oropharyngeal microbiome in Mexican PLHIV with sustained virologic control and immune reconstitution. Oral and oropharyngeal samples were obtained by rinsing and gargling, and participants were classified into HPV-negative, α-HPV (PGMY primers), and β-HPV (FAP primers) groups. The V3–V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. A total of 65 participants were included in the final analysis: 19 HPV-negative, 16 -α-HPV positive (PGMY primers), and β-HPV positive (FAP primers). Bacterial Alpha diversity of the oral microbiome was significantly higher in both α-HPV- positive and β-HPV positive groups than in the HPV-negative group, with the highest diversity observed in the α-HPV positive group. The α-HPV group also showed a higher Fusobacteriota/Bacteroidota ratio and enrichment of Fusobacteriota-related taxa. In addition, predicted functional analysis showed enrichment of pathways related to lysine and pyruvate fermentation to butyrate in the α-HPV(PGMY primers) group. These findings suggest that α- and β-HPV infections may be associated with different oral microbial ecosystems in PLHIV.