The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study
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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
- Brazil
- 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
- endometriosis endometriosis,Endometriosis (clinical),endometriosis (disease),Endometriosis (disorder),Endometriosis (morphologic abnormality),ENDOMETRIOSIS NEC,Endometriosis NOS,Endometriosis NOS (disorder),Endometriosis of other specified sites,Endometriosis, site unspecified
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Stage 1/2 Endometriosis patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage 3/4 Endometriosis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). This study was comparing patients with different stages of endometriosis to each other.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Participants were excluded if they had taken antibiotics within the past 3 months
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
- Statistical test
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Figure 4 and Discussion section
Description: Patients with stage 3/4 endometriosis had a higher abundance of Anaerococcus than those with stage1/2 endometriosis. Other signatures could not be reported because the rest of the paper grouped OTUs into community state types (CSTs).
Abundance in Group 1: increased abundance in Stage 3/4 Endometriosis patients
NCBI | Quality Control | Links |
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Anaerococcus |
Revision editor(s): Samara.Khan
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- endometriosis endometriosis,Endometriosis (clinical),endometriosis (disease),Endometriosis (disorder),Endometriosis (morphologic abnormality),ENDOMETRIOSIS NEC,Endometriosis NOS,Endometriosis NOS (disorder),Endometriosis of other specified sites,Endometriosis, site unspecified
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower stages of endometriosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher stages of endometriosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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: Fig 3B
Description: The top contributing OTU features for this model, ranked by Mean Decreased Accuracy.
Abundance in Group 1: decreased abundance in Higher stages of endometriosis
NCBI | Quality Control | Links |
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Porphyromonas | ||
Neisseria | ||
Haemophilus |
Revision editor(s): Atrayees
Signature 2
Source: Fig 3B
Description: The top contributing OTU features for this model, ranked by Mean Decreased Accuracy.
Abundance in Group 1: increased abundance in Higher stages of endometriosis
NCBI | Quality Control | Links |
---|---|---|
Anaerococcus | ||
Acidovorax | ||
Sphingomonas | ||
Peptoniphilus | ||
Dialister | ||
Phyllobacterium | ||
Howardella | ||
Escherichia | ||
Lactobacillus | ||
Varibaculum | ||
Propionibacterium |
Revision editor(s): Atrayees