Oral Microbiome Alterations Associated with Human Papillomavirus Infection in Edo State, Nigeria: A 16S rRNA Metagenomic Study
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Date
2025-12
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Lead City University Ibadan
Abstract
Understanding the oral microbiome's interplay with Human Papillomavirus (HPV) and Human Immunodeficiency Virus (HIV) is crucial for elucidating HPV-related disease pathogenesis. However, over 90% of HPV–microbiome studies originate from high-income countries. A Nigerian-specific microbial signature for HPV-associated dysbiosis is lacking, limiting efforts to develop relevant biomarkers or understand unique disease progression in this population. This study aimed to identify oral microbial signatures associated with HPV infection, hypothesizing distinct alterations due to immunomodulation, particularly when stratified by HIV status. A nested case-control design was employed within the prospective HOMINY cohort in Edo State, Nigeria. Twenty oral rinse samples (10 HPV-positive, 10 HPV-negative), stratified by HIV status, were analyzed via full-length 16S rRNA sequencing on a PacBio Revio platform. Bioinformatics analyses used QIIME 2 for diversity metrics, ANCOM-BC2 for differential abundance (adjusting for age, sex, and HIV status), and PICRUSt2 for functional predictions. Oral HPV prevalence was higher and more diverse in HIV-positive individuals. Alpha diversity showed greater Chao1 richness (β = 455.9, p = 0.050) and Shannon diversity (β = 1.53, p = 0.033) in HIV-negative/HPV-positive individuals, suggesting microbial expansion. Beta diversity showed no significant community-wide differences. Taxonomic richness was highest in HIV-positive/HPV-positive individuals, with enrichment of low-abundance phyla (Spirochaetota, Mycoplasmatota). Bacillota dominated overall, while Bacteroidota increased in HIV-negative/HPV-positive samples. HIV status modified HPV-related microbial shifts: HIV-positive/HPV-positive individuals showed moderate changes (e.g., enriched Nanoperiomorbus, depleted Aggregatibacter), whereas HIV-negative/HPV-positive individuals showed stronger effects (e.g., enriched Nanosynbacter, depleted Moryella). Functional predictions revealed nominal shifts, including enrichment of CRISPR-associated systems and polysaccharide degradation enzymes and depletion of nucleotide metabolism pathways. These findings highlight the context-dependent oral microbiome response to HPV infection and potential biomarkers for HPV-related oral pathologies.
Keywords: HPV, 16s rRNA Metagenomics, Oral microbiome, Oral HPV in Nigeria
Word Count: 275
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Keywords
HPV, 16s rRNA Metagenomics, Oral microbiome, Oral HPV in Nigeria
Citation
Kate Turabian