The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

32656096

DOI Digital object identifier for electronic documents.

10.3389/fcimb.2020.00286

URI

Authors

Yang Q, Wang Y, Wei X, Zhu J, Wang X, Xie X, Lu W

Journal

Frontiers in cellular and infection microbiology

Year

2020

Keywords:

HPV infection, cervical cancer, metabolism, shotgun metagenomic sequencing, vaginal microbiome

The association of microbiome imbalance with cancer development is being one of the research hotspots. Persistent HPV infection is a causal event in cervical cancer initiation, but, little is known about the microbiome composition and function in HPV infection. Here we identified the compositional and functional alterations on vaginal samples from 27 HPV16 positive women and 25 age-matched HPV negative controls using shotgun metagenomic sequencing, to provide a comprehensive investigation describing the microbial abundances and enriched metabolic functions in cervicovaginal metagenomes. We further employed qPCR assays to evaluate two selected gene markers of HPV16 infection in an independent validation cohort consisting of 88 HPV16 positive women and 81 controls, and six selected species markers in a subset of validation cohort of 45 HPV16 positive women and 53 controls. We found that the relative abundance of dominant Firmicutes was lower, Actinobacteria, Fusobacteria and viruses phyla were significantly higher in the HPV16-positive group; 77 genera including Gardnerella, Peptostreptococcus, and Prevotella were higher, and 20 genera including Lactobacillus and Aerococcus were lower in the HPV16-positive women. Abundance of 12 genes, 17 genera, and 7 species biomarkers showed an excellent predictive power for the HPV16-positive individuals, with 0.861, 0.819, and 0.918, respectively, of the area under the receiver-operating characteristic curve (AUC). We further characterized the microbial function, and revealed that HPV16-positive women were enriched in metabolism and membrane transport, and depleted by glycan biosynthesis and metabolism, and replication and repair. Quantitative PCR measurements validated that one gene marker and three species were significantly enriched in HPV16-positive women. These results highlight a fundamental fact that there are altered composition and function of the vaginal microbiome in HPV16-positive women, suggesting that vaginal dysbiosis may be associated with HPV infection in the female genital tract.

Experiment 1

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Curated date: 2021/03/21

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Cervicovaginal secretion, Posterior fornix of vagina Cervicovaginal secretion,Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy control
Group 1 name Corresponds to the case (exposed) group for case-control studies: HPV-16+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with HPV-16 confirmed by HPV genotyping assay
Group 0 sample size Number of subjects in the control (unexposed) group: 25
Group 1 sample size Number of subjects in the case (exposed) group: 27
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

Lab analysis

Sequencing type: WMS

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Signature 1

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Mark reviewed

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Needs review

Curated date: 2021/03/21

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 3

Description: Vaginal microbiome as HPV16-infection markers.

Abundance in Group 1: increased abundance in HPV-16+

NCBI	Quality Control	Links
Nocardia brevicatena
Prevotella melaninogenica
Dialister invisus
Pedobacter panaciterrae
Olsenella uli
Prevotella corporis
Kytococcus sedentarius
Fusobacterium nucleatum
Streptomyces auratus
Prevotella amnii
Solobacterium moorei
Parvimonas micra
Prevotella bivia
Prevotella disiens
Schaalia turicensis
Peptoniphilus harei
Paracoccus denitrificans
Dialister micraerophilus
Atopobium deltae
Veillonella montpellierensis
Chlamydia trachomatis
Stutzerimonas stutzeri
Mageeibacillus indolicus
Anaerococcus tetradius
Gemella asaccharolytica
Peptoniphilus lacrimalis
Mobiluncus curtisii
Peptostreptococcus anaerobius
Gardnerella vaginalis

Revision editor(s): Cynthia Anderson