Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W, Qiu L
Journal
BMC infectious diseases
Year
2020
Keywords:
Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome
BACKGROUND: In this study, the association between human papillomavirus (HPV) infection and related cervical intraepithelial neoplasia (CIN) or cervical cancer and vaginal microbiome was evaluated in Chinese cohorts. METHODS: The vaginal bacterial composition of five groups, HPV-infected women without CINs (HPV, n = 78), women with low-grade squamous intraepithelial lesions (LSIL, n = 51), women with high-grade squamous intraepithelial lesions (HSIL, n = 23), women with invasive cervical cancer (Cancer, n = 9) and healthy women without HPV infection (Normal, n = 68), was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V3-4) using Illumina MiSeq. RESULTS: HPV infection increased vaginal bacterial richness and diversity regardless of the status of CINs. The vaginal bacterial richness and diversity were further augmented in women with cervical cancer. Lactobacillus was the most abundant genus in all groups. HPV infection had a negative influence on the abundances of Lactobacillus, Gardnerella and Atopobium. Accordingly, HPV infection increased the relative abundance of Prevotella, Bacillus, Anaerococcus, Sneathia, Megasphaera, Streptococcus and Anaerococcus. The increased proportions of Bacillus, Anaerococcus and the reduced abundance of Gradnerella vaginalis were probably related with the progression of CINs severity. HPV infection without CINs or cancerous lesions was strongly associated with Megasphaera. The most abundant bacterium in the LSIL group was Prevotella amnii. However, Prevotella timonensis, Shuttleworthia and Streptococcaceae at the family level were three taxa related to HSIL. Furthermore, more taxa were associated with the Cancer group including Bacillus, Sneathia, Acidovorax, Oceanobacillus profundus, Fusobacterium, Veillonellaceae at the family level, Anaerococcus and Porphyromonas uenonis. Samples in the Normal group were mostly assigned to CST III. HPV infection converted the vaginal bacterial community structure from CST III to CST IV. Furthermore, the proportions of CST IV were gradually augmented with the progression of the severity of CINs. CONCLUSIONS: This work interpreted the differential vaginal bacteria under HPV infection and various precancerous or cancerous lesions in a Chinese cohort. We distinguished the specific microbes and the vaginal bacterial structure that were related with the progression of CINs severity in Chinese women.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Curated date: 2021/03/20
Curator: Cynthia Anderson
Revision editor(s): WikiWorks, Cynthia Anderson, Atrayees, Peace Sandy
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior 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,Human papilloma virus infection
- 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 +
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV-infected women without CIN confirmed by HPV genotyping test and examination
- Group 0 sample size Number of subjects in the control (unexposed) group
- 68
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 14 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Source: Figure 5
Description: The unique taxa and microbiomarkers for different groups
Abundance in Group 1: increased abundance in HPV +
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera |
Revision editor(s): Cynthia Anderson
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Curated date: 2021/03/20
Curator: Cynthia Anderson
Revision editor(s): Cynthia Anderson, WikiWorks, Victoria
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- women with low-grade squamous intraepithelial lesions confirmed by biopsy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Source: Figure 5
Description: The unique taxa and microbiomarkers for different groups
Abundance in Group 1: increased abundance in LSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella amnii |
Revision editor(s): Cynthia Anderson
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Curated date: 2021/03/20
Curator: Cynthia Anderson
Revision editor(s): Cynthia Anderson, WikiWorks, Victoria
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- women with high-grade squamous intraepithelial lesions confirmed by biopsy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 68
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Source: Figure 5
Description: The unique taxa and microbiomarkers for different groups
Abundance in Group 1: increased abundance in HSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Clostridia | ||
| Eubacteriales | ||
| Prevotellaceae | ||
| Lachnospiraceae | ||
| Shuttleworthella | ||
| Streptococcaceae | ||
| Hoylesella timonensis |
Revision editor(s): Cynthia Anderson
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Curated date: 2021/03/20
Curator: Cynthia Anderson
Revision editor(s): Cynthia Anderson, WikiWorks, Victoria
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical cancer cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,Cervical cancer,cervical cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cervical cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- women with cervical cancer confirmed by biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Source: Figure 5
Description: The unique taxa and microbiomarkers for different groups
Abundance in Group 1: increased abundance in cervical cancer
Revision editor(s): Cynthia Anderson
Experiment 5
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Differences from previous experiment shown
Subjects
- 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,Human papilloma virus infection
- 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+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV-infected women without CIN confirmed by HPV genotyping test and examination
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Source: Fig 3, 4
Description: Relative abundance of taxa across the samples
Abundance in Group 1: increased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Fusobacteriia | ||
| Pseudomonadota | ||
| Prevotella | ||
| Bacillus | ||
| Sneathia | ||
| Megasphaera | ||
| Streptococcus | ||
| Anaerococcus |
Revision editor(s): Atrayees
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Source: Figure 3, 4
Description: Relative abundance of taxa across the samples
Abundance in Group 1: decreased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Atopobium |
Revision editor(s): Atrayees
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