Metagenomic insight into the vaginal microbiome in womeninfected with HPV 16 and18

npj biofilms and microbiomes

Da-Ryung Jung(1),Yeseul Choi(2,3), Minsoo Jeong(1), Vineet Singh(1), Se Young Jeon(4,5), Incheol Seo(5,6), Nora Jee-Young Park(5,7), Yoon Hee Lee(4), Ji Young Park(7), Hyung Soo Han(2,3,5,8),Jae-Ho Shin(1,9), Gun Oh Chong(4,5,*)

1 Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea

2 Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, Republic of Korea

3 BK21 Four Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.

4 Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea

5 Clinical Omics Institute, Kyungpook National University, Daegu, Republic of Korea

6 Department of Immunology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea

7 Department of Pathology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea

8 Department of Physiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea

9 NGS Core Facility, Kyungpook National University, Daegu, Republic of Korea

* Correspondence

Human papillomavirus (HPV) 16 and 18 (HPV 16/18) account for over 70% of cervical cancer (CC) cases, yet their interaction with the vaginal microbiome (VM) remains unclear. This study explored the association between high-risk HPV types (HR-HPVs), VM composition and bacterial function using shotgun metagenomic sequencing. In early-stage cervical lesions, the HPV 16/18 group showed reduced Lactobacillus-dominant community state types compared to other HR-HPVs, while invasive CC exhibited increased pathogenic bacteria, including Streptococcus agalactiae, Fannyhessea vaginae, and Sneathia vaginalis. The VM associated with HPV 16/18 was enriched in immune response and inflammation pathways, whereas other HR-HPVs were linked to cellular metabolism and hormonal signaling. Notably, HPV 16/18 exhibited stronger bacterial-fungal correlations, indicating shifts in the microbial community. Furthermore, 137 metagenome-assembled genomes provided insights into unique microbial genomic signatures. Our study links VM differences with HPV 16/18 oncogenic potential across cervical lesion stages, urging further research for better diagnostics and treatments.

Clinical microbiology, Metagenomics

10.1038/s41522-025-00747-1