Microbiota composition and distribution along the female reproductive tract of women with endometriosis
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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 (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lower part of vagina Caudal vagina,Lower third of vagina,Lower vagina,Perineal part of vagina,Sinus vagina,Vagina lower part,Vaginal bulb,Lower part of 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
- Controls undergoing laparoscopic surgery for benign tumors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Endometriosis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This experiment only curates unknown species up to the genus level so it needs to be deleted.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- This experiment only curates unknown species up to the genus level so it needs to be deleted.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Signature 1
Source: Figure 2 and Results section
Description: Created in error - this figure only curates unidentified species up to the genus level. This experiment needs to be deleted.
Abundance in Group 1: increased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Samara.Khan
Experiment 2
Subjects
- 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
- 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).
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients were excluded if they had taken antibiotics within 6 months before the study
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2 and Results section
Description: Lactobacillus iners was decreased in the posterior fornix of the vagina of endometriosis patients compared to controls.
Abundance in Group 1: decreased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 2 and Results section
Description: Created in error - this signature only curates unidentified species up to the genus level. This signature needs to be deleted.
Abundance in Group 1: increased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Samara.Khan
Experiment 3
Subjects
- 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
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2 and Results section
Description: The following taxa were increased in the cervical mucus of endometriosis patients compared to control patients.
Abundance in Group 1: increased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Caulobacteraceae | ||
| Comamonadaceae | ||
| Erysipelotrichaceae | ||
| Lactobacillus iners | ||
| Leptotrichiaceae | ||
| Pseudomonadaceae | ||
| Pseudomonas viridiflava |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 2 and Results section
Description: The following taxa were decreased in the cervical mucus of endometriosis patients compared to controls. Some species were unidentified and were excluded from curation
Abundance in Group 1: decreased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Micrococcaceae | ||
| Pseudomonas viridiflava |
Revision editor(s): Samara.Khan
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Endometrium Tunica mucosa (endometrium),Tunica mucosa uteri,Uterine endometrium,Uterine mucosa,Uterine mucous membrane,Endometrium
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2 and Results section
Description: The following taxa were increased in the endometrium of endometriosis patients compared to controls.
Abundance in Group 1: increased abundance in Endometriosis patients
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 2 and Results section
Description: The following taxa were decreased in the endometrium of endometriosis patients compared to controls.
Abundance in Group 1: decreased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichaceae | ||
| Tissierellaceae | ||
| Stenotrophomonas acidaminiphila |
Revision editor(s): Samara.Khan
Experiment 5
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Peritoneal fluid Peritoneal fluid
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2 and Results section
Description: The following taxa were increased in the peritoneal fluid of endometriosis patients compared to controls.
Abundance in Group 1: increased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter guillouiae | ||
| Clostridium | ||
| Enterobacteriaceae | ||
| Micrococcaceae | ||
| Pseudomonadaceae | ||
| Pseudomonas viridiflava | ||
| Sphingobacterium multivorum |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 2 and Results section
Description: The following taxa were decreased in the peritoneal fluid of endometriosis patients compared to controls.
Abundance in Group 1: decreased abundance in Endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas fragi |
Revision editor(s): Samara.Khan
