Table 1.

Summary of representative included studies investigating HPV-microbiota associations across oral, anorectal and penile mucosal sites.

Anatomical site	Study population	Sample size	Study design	Specimen type	Sequencing/method	Main findings	References
Oral	US adults from nationally representative NHANES	N=5496	Cross-sectional	Oral rinse	16S rRNA (V4 region), QIIME; multivariable logistic regression	Reduced oral α-diversity was independently associated with high-risk oral HPV only among males. Significant β-diversity differences by high-risk HPV status were also restricted to males.	Feng et al. (2024)
Oral	Adult participants; stratified by periodontitis status	N=4685	Cross-sectional	Oral rinse	16S rRNA amplicon sequencing; adjusted logistic regression	Moderate-to-severe periodontitis was associated with higher odds of oral HPV infection only in females.	Liang et al. (2026)
Oral	Pregnant women (third trimester)	N=39	Cross-sectional	Maternal oral swabs	16S rRNA V3-V4 amplicon sequencing; QIIME, LEfSe	Higher bacterial richness in HPV-positive maternal oral samples. Selenomonas spp., Megasphaera and TM7 taxa enriched in HPV-positive oral specimens.	Tuominen et al (2018a)
Oral	Risk-enrolled adult participants from MOUTH study*	N=495	Cross-sectional	Saliva; oral-rinse	16S rRNA V4 amplicon sequencing; PICRUSt2; Corncob differential abundance analysis	Significant shifts in β-diversity were observed. HPV-positive subjects had higher abundance of Actinomycetaceae, Prevotellaceae, Veillonellaceae, Campylobacteraceae and Bacteroidete.	Zhang et al. (2022)
Oral	Adults with non-cancer oral HPV status	N=127	Cross-sectional (re-analysis of publicly available data)	Oral swab	Full-length 16S rRNA sequencing; ecotype clustering; VFDB-based inferred virulence-ecology profiling	Oral HPV did not drive discrete oral-microbiome taxa shifts or define microbiome ecotypes. HPV-positivity aligned with pre-existing high-virulence-pressure oral ecological landscapes rather than reshaping community composition.	Chambuso et al. (2026)
Oral	US adults from NHANES 2009-2012	N=5534	Cross-sectional	Oral rinse	16S rRNA V4 amplicon sequencing; LDA topic-modelling, ADAPT differential-abundance analysis	Higher α-diversity was observed in HPV-positive Non-Hispanic Black participants. Sneathia and Odoribacterium were enriched among HPV-positive individual.	Byrd et al. (2026)
Oral	HIV-negative and HIV-positive MSM	N=63	Cross-sectional	Oral swabs	16S rRNA amplicon sequencing	HrHPV-linked oral microbial alterations were only detectable in HIV-negative MSM. Pre-existing HIV-associated oral dysbiosis may mask HPV-specific microbial signature.	Escobar-Marcillo et al. (2025)
Oral	Healthy Australian adults (stratified by HPV-negative, low-risk HPV, high-risk HPV status)	N=127	Cross-sectional retrospective analysis	Saliva	PacBio HiFi full-length 16S rRNA gene sequencing; QIIME2, DESeq2	HPV-negative males harboured higher Streptococcus salivarius; lr-HPV-positive males showed depletion of S. salivarius and S. parasanguinis. HPV-positive females had significantly lower Shannon α-diversity and distinct oral β-diversity.	Maidment et al. (2025)
Oral	Breastfeeding mothers and their infants (mother-infant pairs)	N=35	Cross-sectional	Breast-milk; infant oral swabs	16S rRNA V3-V4 amplicon sequencing; QIIME, LEfSe	Infant oral HPV infection altered bacterial community clustering without changing overall α-diversity. Ureaplasma, Lysinibacillus enriched in HPV-positive infants; Veillonella dispar enriched in HPV-negative infants.	Tuominen et al. (2018b)
Anorectal	HIV-negative MSM	N=58	Retrospective analysis based on prospective cohort follow-up	Rectal swabs	16S rRNA (V3-V4 region), QIIME2 pipeline; Wilcoxon test, Metastats, LEfSe	Bacteroides fragilis was significantly enriched in participants with persistent anal HPV. Victivallis, Negativibacillus, Eggerthella were enriched in persistent-HPV subjects; Prevotella disiens and Gardnerella were more abundant in HPV-negative participant.	Yang et al. (2025)
Anorectal	Nigerian MSM	N=113	Cross-sectional pilot study	Anal swabs	16S rRNA (V3-V4 region, Illumina MiSeq); K-means clustering, LEfSe, Fisher’s exact test	Four anorectal microbial community clusters were identified. The Sneathia-enriched cluster had the highest proportion of HPV-16-positive participants; most subjects in this cluster were ART-treated, virally-suppressed MSM.	Nowak et al. (2019)
Anorectal	Women with high-grade lower-genital-tract lesions	N=71	Retrospective analysis	Anorectal swabs	16S rRNA V4 amplicon sequencing (Illumina MiSeq), QIIME2, LEfSe, UniFrac-based PCoA	Pro-inflammatory anaerobes including Peptoniphilus, Prevotella, Porphyromonas and Fusobacterium were significantly enriched in anal-cancer specimens.	Elnaggar et al. (2023)
Anorectal	STI-clinic-attending MSM	N=92	Cross-sectional	Anorectal swabs	16S rRNA (V3-V4 region, Illumina MiSeq); QIIME pipeline; point-biserial correlation	Hr-HPV positivity was positively correlated with Escherichia and Corynebacterium, and negatively correlated with multiple Firmicutes taxa including Prevotella, Oscillospira, Sutterella. Elevated α-diversity was observed in CT/NG-infected HPV-positive subjects.	Ceccarani et al. (2024)
Penile	Heterosexually-active Black South African adult men	N=238	Cross-sectional retrospective analysis	Swabs of penile shaft, glans and coronal sulcus	16S rRNA (V3-V4 region), Illumina MiSeq; LEfSe for differential taxa analysis	Six penile CSTs were identified. Corynebacterium-dominated CST-1 correlated with lower hr-HPV risk, whereas anaerobe-rich CST-5 was associated with higher HPV/hr-HPV prevalence. Enrichment of Prevotella, Peptoniphilus, Dialister and depletion of Corynebacterium were observed in hr-HPV-positive men.	Onywera et al (2020a)
Penile	Sexually-active HIV-negative men	N=103	Cross-sectional	Penile skin swabs	16S rRNA V4-region amplicon sequencing; hierarchical clustering for CSTs	Subclinical HPV infection in HIV-negative men was associated with a dysbiotic PSM, characterized by an increased abundance of anaerobic bacteria alongside with a reduced proportion of facultative anaerobic genera.	Garza-González et al. (2026)

MSM, men who have sex with men; hr-HPV, high risk HPV; lr-HPV, low risk HPV; CST, Community State Type.

*MOUTH study, The Men and Women Offering Understanding of Throat HPV study.