Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women
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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
Experiment 1
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
- Uterine cervix Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
- 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
- Baseline HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Baseline HPV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 90
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status
Abundance in Group 1: increased abundance in Baseline HPV+
NCBI | Quality Control | Links |
---|---|---|
Mollicutes | ||
Mycoplasmatota | ||
Mycoplasmatales | ||
Mycoplasmataceae | ||
Ureaplasma |
Revision editor(s): WikiWorks
Signature 2
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status
Abundance in Group 1: decreased abundance in Baseline HPV+
NCBI | Quality Control | Links |
---|---|---|
Coxiellaceae | ||
Deinococci | ||
Deinococcota | ||
Ectothiorhodospiraceae | ||
Ezakiella | ||
Faecalibacterium | ||
Fusobacteriaceae | ||
Fusobacterium | ||
Listeriaceae | ||
Rickettsiella | ||
Fusobacteriales |
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no new acquisition of HPV within a year
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- new acquisition of HPV within a year
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- New HPV-type acquisition confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 109
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status
Abundance in Group 1: decreased abundance in new acquisition of HPV within a year
NCBI | Quality Control | Links |
---|---|---|
Actinomyces |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- with at least one HPV type cleared in a year
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- without any HPV type cleared
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- No HPV-type cleared confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 75
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status
Abundance in Group 1: decreased abundance in without any HPV type cleared
NCBI | Quality Control | Links |
---|---|---|
Paracoccaceae | ||
Rhodobacterales |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- 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
- HPV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 90
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level
Abundance in Group 1: increased abundance in HPV+
NCBI | Quality Control | Links |
---|---|---|
Ureaplasma parvum |
Revision editor(s): WikiWorks
Signature 2
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level
Abundance in Group 1: decreased abundance in HPV+
NCBI | Quality Control | Links |
---|---|---|
Ezakiella massiliensis | ||
Pseudomonas aeruginosa |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no new acquisition of HPV within a year
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- new acquisition of HPV within a year
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- New HPV-type acquisition confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 109
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level
Abundance in Group 1: increased abundance in new acquisition of HPV within a year
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella tannerae | ||
Prevotella nigrescens | ||
Segatella oulorum | ||
Dialister invisus |
Revision editor(s): WikiWorks
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- with any HPV type cleared in a year
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- without any HPV type cleared
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- No HPV-type cleared confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 75
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level
Abundance in Group 1: increased abundance in without any HPV type cleared
NCBI | Quality Control | Links |
---|---|---|
Gemelliphila asaccharolytica | ||
Prevotella amnii | ||
Labilithrix luteola | ||
Lachnotalea glycerini |
Revision editor(s): WikiWorks
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no HPV type persisted
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- at least one HPV type persisted
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Any HPV-type persisted confirmed by HPV assay and genotyping
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level
Abundance in Group 1: increased abundance in at least one HPV type persisted
NCBI | Quality Control | Links |
---|---|---|
Hoylesella timonensis | ||
Microvirga lupini | ||
Dialister invisus | ||
Coprococcus comes | ||
Deinococcus radiopugnans | ||
Anaerobacterium chartisolvens |
Revision editor(s): WikiWorks
Signature 2
Source: figure 3
Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level
Abundance in Group 1: decreased abundance in at least one HPV type persisted
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus delbrueckii |
Revision editor(s): WikiWorks