Microbiota composition and distribution along the female reproductive tract of women with endometriosis
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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 Uniform resource identifier for web resources.
Authors
Wei W, Zhang X, Tang H, Zeng L, Wu R
Journal
Annals of clinical microbiology and antimicrobials
Year
2020
Endometriosis (EMS) is a multifactorial disease that affects 10%-15% women of reproductive age and is associated with chronic pelvic pain and infertility. The pathogenesis of EMS has not been consistently explained until now. In this study, we involved 36 endometriosis patients and 14 control subjects who performed laparoscopic surgery due to gynecological benign tumor. The samples from lower third of vagina (CL), posterior vaginal fornix (CU), cervical mucus (CV), endometrium (ET) and peritoneal fluid (PF), were collected and sequenced by 16S rRNA amplicon. The continuous change of the microbiota distribution was identified along the reproductive tract. The flora in lower reproductive tract (CL, CU) were dominated by Lactobacillus. Significant difference of the community diversity began showing in the CV of EMS patients and gradually increased upward the reproductive tract. It indicates the microbiota in cervical samples is expected to be an indicator for the risk of EMS. This study also highlights the decreasing of Lactobacillus in vaginal flora and the increasing of signature Operational Taxonomic Units (OTUs) in transaction zone (CV) and upper reproductive tract (ET, PF) of EMS patients, which reflect the alteration of microbial community associated with EMS, participation of specific colonized bacteria in the EMS pathogenesis and relationship between microbiota and development of disease.
Experiment 1
Needs review
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
Needs review
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 | Links |
|---|
Revision editor(s): Samara.Khan
Experiment 2
Needs review
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
- Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix 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
- 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).
- 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)
- Patients were excluded if they had taken antibiotics within 6 months before the study
Lab analysis
- Sequencing type
- 16S
- 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
Needs review
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 | Links |
|---|---|
| Lactobacillus iners |
Revision editor(s): Samara.Khan
Signature 2
Needs review
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 | Links |
|---|
Revision editor(s): Samara.Khan
Experiment 3
Needs review
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
- 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
- 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
- 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).
- 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)
- Patients were excluded if they had taken antibiotics within 6 months before the study
Lab analysis
- Sequencing type
- 16S
- 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
Needs review
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 | Links |
|---|---|
| Caulobacteraceae | |
| Comamonadaceae | |
| Erysipelotrichaceae | |
| Lactobacillus iners | |
| Leptotrichiaceae | |
| Pseudomonadaceae | |
| Pseudomonas viridiflava ⚠ |
Revision editor(s): Samara.Khan
Signature 2
Needs review
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 | Links |
|---|---|
| Micrococcaceae | |
| Pseudomonas viridiflava ⚠ |
Revision editor(s): Samara.Khan
Experiment 4
Needs review
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
- Endometrium Tunica mucosa (endometrium),Tunica mucosa uteri,Uterine endometrium,Uterine mucosa,Uterine mucous membrane,Endometrium
- 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
- 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).
- 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)
- Patients were excluded if they had taken antibiotics within 6 months before the study
Lab analysis
- Sequencing type
- 16S
- 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
Needs review
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
Needs review
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 | Links |
|---|---|
| Erysipelotrichaceae | |
| Tissierellaceae | |
| Stenotrophomonas acidaminiphila ⚠ |
Revision editor(s): Samara.Khan
Experiment 5
Needs review
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
- Peritoneal fluid Peritoneal fluid
- 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
- 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).
- 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)
- Patients were excluded if they had taken antibiotics within 6 months before the study
Lab analysis
- Sequencing type
- 16S
- 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
Needs review
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 | Links |
|---|---|
| Acinetobacter guillouiae ⚠ | |
| Clostridium | |
| Enterobacteriaceae | |
| Micrococcaceae | |
| Pseudomonadaceae | |
| Pseudomonas viridiflava ⚠ | |
| Sphingobacterium multivorum ⚠ |
Revision editor(s): Samara.Khan
Signature 2
Needs review
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 | Links |
|---|---|
| Pseudomonas fragi ⚠ |
Revision editor(s): Samara.Khan
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