Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion
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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
- Controls undergoing laparoscopic surgery for benign conditions
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Confirmed endometriosis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- within 30 days prior to sample collection
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 4B
Description: There was increased abundance of gemella and streptococcus when comparing the vaginal fluid of endometriosis patients to healthy controls
Abundance in Group 1: increased abundance in Confirmed endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Streptococcus |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 4B
Description: There was decreased abundance of aerococcus in vaginal fluid of endometriosis patients compared to healthy controls. Atopobium, which is normally found in the lower female reproductive tract, was completely absent in vaginal fluid of endometriosis patients.
Abundance in Group 1: decreased abundance in Confirmed endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Atopobium |
Revision editor(s): Samara.Khan
Experiment 2
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 4B
Description: There was increased abundance of bifidobacterium when comparing the endometrial lining of endometriosis patients to healthy controls
Abundance in Group 1: increased abundance in Confirmed endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 4B
Description: There was decreased abundance of atopobium, mobiluncus, campylobacter, chromohalobacter, and alcanivorax when comparing the endometrial lining of endometriosis patients to healthy controls
Abundance in Group 1: decreased abundance in Confirmed endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alcanivorax | ||
| Atopobium | ||
| Campylobacter | ||
| Chromohalobacter | ||
| Mobiluncus |
Revision editor(s): Samara.Khan
Experiment 3
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 4B
Description: When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were increased: aerococcus, staphylococcus, sphingomonas, alishewanella, pseudomonas, and enterococcus
Abundance in Group 1: increased abundance in Confirmed endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Staphylococcus | ||
| Sphingomonas | ||
| Alishewanella | ||
| Pseudomonas | ||
| Enterococcus |
Revision editor(s): Samara.Khan
Signature 2
Source: Figure 4B
Description: When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were decreased: prevotella, atopobium, afipia, mobiluncus, campylobacter, and facklamia
Abundance in Group 1: decreased abundance in Confirmed endometriosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Atopobium | ||
| Afipia | ||
| Mobiluncus | ||
| Campylobacter | ||
| Facklamia |
Revision editor(s): Samara.Khan
