Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort 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
- Australia
- 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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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,Endometriosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Endometriosis and Non-endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy control cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the healthy control cohort were women with no known gynaecological symptoms or infertility concerns.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
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
- 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
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis
Abundance in Group 1: increased abundance in Healthy control cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Butyrivibrio | ||
| Lactococcus | ||
| Lautropia | ||
| Neisseria | ||
| Neisseriaceae | ||
| Peptostreptococcaceae | ||
| Prevotella |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control and Non-endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Endometriosis cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the endometriosis cohort were women who were confirmed to have endometriosis.
- 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
- 21
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis
Abundance in Group 1: increased abundance in Endometriosis cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| bacterium F16 | ||
| Actinomycetaceae |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control and endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-endometriosis cohorts
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the non-endometriosis cohort were women who had confirmed gynaecological pathologies such as fibroids, abnormal uterine bleeding and ovarian cysts.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis
Abundance in Group 1: increased abundance in Non-endometriosis cohorts
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Bifidobacterium | ||
| Lactobacillus |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Endometriosis and Non-endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy control cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the healthy control cohort were women with no known gynaecological symptoms or infertility concerns.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis
Abundance in Group 1: increased abundance in Healthy control cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Lachnospira | ||
| Butyricicoccus | ||
| Victivallaceae | ||
| Peptococcaceae | ||
| Bacteria | ||
| RF39RF39 | ||
| RF32RF32 |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control and Non-endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Endometriosis cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the endometriosis cohort were women who were confirmed to have endometriosis.
- 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
- 21
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis
Abundance in Group 1: increased abundance in Endometriosis cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium | ||
| Lactobacillus | ||
| Haemophilus |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control and endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-endometriosis cohorts
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the non-endometriosis cohort were women who had confirmed gynaecological pathologies such as fibroids, abnormal uterine bleeding and ovarian cysts.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis
Abundance in Group 1: increased abundance in Non-endometriosis cohorts
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium | ||
| Bacteroidales |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Endometriosis and Non-endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy control cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the healthy control cohort were women with no known gynaecological symptoms or infertility concerns.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis.
Abundance in Group 1: increased abundance in Healthy control cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Salmonella | ||
| Listeria | ||
| Pseudomonas | ||
| Bacillus |
Revision editor(s): MyleeeA
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control and Non-endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Endometriosis cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the endometriosis cohort were women who were confirmed to have endometriosis.
- 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
- 21
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis.
Abundance in Group 1: increased abundance in Endometriosis cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Enterococcus | ||
| Tepidimonas | ||
| Thermus |
Revision editor(s): MyleeeA
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control and endometriosis cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-endometriosis cohorts
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the non-endometriosis cohort were women who had confirmed gynaecological pathologies such as fibroids, abnormal uterine bleeding and ovarian cysts.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis.
Abundance in Group 1: increased abundance in Non-endometriosis cohorts
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia | ||
| Haemophilus | ||
| Prevotella | ||
| Weeksellaceae |
Revision editor(s): MyleeeA
Experiment 10
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Minimal/Mild endometriosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate/Severe endometriosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who underwent laparoscopy with confirmed endometriosis (ENDO) Stages 3 and 4 further grouped as Moderate/Severe endometriosis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Figure 6
Description: Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in oral samples.
Abundance in Group 1: increased abundance in Moderate/Severe endometriosis
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 6
Description: Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in oral samples.
Abundance in Group 1: decreased abundance in Moderate/Severe endometriosis
| NCBI | Quality Control | Links |
|---|---|---|
| Cardiobacterium |
Revision editor(s): MyleeeA
Experiment 11
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6
Description: Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in stool samples.
Abundance in Group 1: increased abundance in Moderate/Severe endometriosis
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Paraprevotella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 6
Description: Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in stool samples.
Abundance in Group 1: decreased abundance in Moderate/Severe endometriosis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces |
Revision editor(s): MyleeeA
Experiment 12
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6
Description: Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in vaginal samples.
Abundance in Group 1: increased abundance in Moderate/Severe endometriosis
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Dorea | ||
| Collinsella | ||
| Eubacterium |
Revision editor(s): MyleeeA
