Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Quality issues
Experiment 1
Curated date: 2021/03/18
Curator: Cynthia Anderson
Revision editor(s): Fatima, 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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- persistent HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANOVA
- 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
Signature 1
Source: Figure 3A
Description: Differential florae types in the comparison of the microbiota between high-risk human papillomavirus (HPV) persistent infection higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
Revision editor(s): Fatima, Cynthia Anderson
Experiment 2
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- transient HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection (HPV has regressed within 1 year) with high grade squamus intraepithelial lesion
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANOVA
- 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
Signature 1
Source: Figure 3B
Description: comparison of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group
Abundance in Group 1: decreased abundance in transient HPV+ with HSIL
| NCBI | Links |
|---|---|
| Xanthomonadaceae | |
| [Clostridium] innocuum ⚠ |
Revision editor(s): Cynthia Anderson
Experiment 3
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- transient HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection (HPV has regressed within 1 year) with low grade squamus intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANOVA
- 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
Signature 1
Source: Figure 3C
Description: Comparison of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group
Abundance in Group 1: decreased abundance in transient HPV+ with LSIL
| NCBI | Links |
|---|---|
| Sneathia | |
| Shuttleworthia | |
| Veillonella | |
| [Clostridium] innocuum ⚠ | |
| Megasphaera | |
| Devosia ⚠ | |
| Xanthomonadaceae | |
| Gardnerella ⚠ |
Revision editor(s): Cynthia Anderson
Experiment 4
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV persistent infection with high grade squamus intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANOVA
- 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
Signature 1
Source: Figure 3D
Description: Comparison of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
| NCBI | Links |
|---|---|
| Megasphaera | |
| Peptostreptococcus | |
| Shuttleworthia | |
| Sneathia |
Revision editor(s): Fatima, Cynthia Anderson
Experiment 5
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- persistent HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion
Signature 1
Source: Figure 4A
Description: Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group
Abundance in Group 1: increased abundance in persistent HPV+ with HSIL
| NCBI | Links |
|---|---|
| Streptococcus agalactiae |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 4A
Description: Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
Revision editor(s): Cynthia Anderson
Experiment 6
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient HPV+ with HSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV persistent infection with low grade squamus intraepithelial lesion
Signature 1
Source: Figure 4B
Description: Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group
Abundance in Group 1: increased abundance in persistent HPV+ with LSIL
| NCBI | Links |
|---|---|
| [Ruminococcus] torques |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 4B
Description: Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group
Abundance in Group 1: decreased abundance in persistent HPV+ with LSIL
| NCBI | Links |
|---|---|
| Porphyromonas | |
| Trichinella pseudospiralis | |
| Quinella | |
| Tyzzerella | |
| Flavobacterium gelidilacus ⚠ | |
| Parabacteroides faecis | |
| Dechloromonas |
Revision editor(s): Cynthia Anderson
Experiment 7
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- transient HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection with high grade squamus intraepithelial lesion
Signature 1
Source: Figure 4C
Description: Abundance analysis of the microbiota between high-risk HPV transient infection with HSIL group and high-risk HPV transient infection with LSIL group
Abundance in Group 1: increased abundance in transient HPV+ with HSIL
| NCBI | Links |
|---|---|
| Flavobacteriia | |
| Flavobacteriales | |
| Cloacibacterium | |
| Lactobacillus | |
| Dyella koreensis | |
| Flavobacterium gelidilacus ⚠ | |
| Dyella | |
| Parabacteroides faecis |
Revision editor(s): Cynthia Anderson
Experiment 8
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- transient HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection with low grade squamus intraepithelial lesion
Signature 1
Source: Figure 4D
Description: Abundance analysis of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group
Abundance in Group 1: decreased abundance in transient HPV+ with LSIL
| NCBI | Links |
|---|---|
| Devosia riboflavina ⚠ | |
| Candidatus Saccharibacteria | |
| Sneathia | |
| Lactobacillus | |
| Pseudomonas ⚠ | |
| Shuttleworthia | |
| Leptotrichiaceae | |
| Oscillospiraceae | |
| Pseudomonadaceae |
Revision editor(s): Cynthia Anderson
Experiment 9
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV persistent infection with low grade squamus intraepithelial lesion
Signature 1
Source: Figure 4E
Description: Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group
Abundance in Group 1: increased abundance in persistent HPV+ with HSIL
| NCBI | Links |
|---|---|
| Solirubrobacterales | |
| Morganella |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 4E
Description: Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
| NCBI | Links |
|---|---|
| Prevotella melaninogenica | |
| Dialister | |
| Lactobacillus equicursoris | |
| Prevotella | |
| Sutterella | |
| Peptostreptococcus | |
| Pseudomonas ⚠ | |
| Peptoniphilus lacrimalis ⚠ | |
| Prevotella disiens | |
| Oscillospiraceae |
Revision editor(s): Cynthia Anderson
