Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study
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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.
Authors
Hicks C, Leonardi M, Chua XY, Mari-Breedt L, Espanda M, El-Omar EM, Condous G, El-Assaad F
Journal
BJOG : an international journal of obstetrics and gynaecology
Year
2024
Keywords:
bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral
OBJECTIVE: To identify a microbial signature for endometriosis for use as a diagnostic non-invasive biomarker. DESIGN: Prospective cohort pilot study. SETTING: Nepean Hospital and UNSW Microbiome Research Centre, Australia. POPULATION: Sixty-four age- and sex-matched subjects (n = 19 healthy control (HC); n = 24 non-endometriosis (N-ENDO) and n = 21 confirmed endometriosis (ENDO)). All study participants, besides healthy controls, underwent laparoscopic surgical assessment for endometriosis, and histology was performed on excised lesions. METHODS: Oral, stool and, vaginal samples were self-collected at a single time point for healthy controls, and preoperatively for patients undergoing laparoscopy. Samples underwent 16S rRNA amplicon sequencing, followed by bioinformatics analysis. MAIN OUTCOME MEASURES: Compositional differences between cohorts as identified by diversity analyses, and differentially abundant microbial taxa, as identified by LEfSE analysis. RESULTS: The composition of the oral (adjusted p = 0.003), and stool (adjusted p = 0.042) microbiota is different between the three cohorts. Differentially abundant taxa are present within each cohort as identified by LEfSE analysis. Particularly, Fusobacterium was enriched in the oral samples of patients with moderate/severe endometriosis. CONCLUSIONS: Taxonomic and compositional differences were found between the microbiota in the mouth, gut and, vagina of patients with and without endometriosis and healthy controls. Fusobacterium was enriched in patients with moderate/severe endometriosis. Fusobacterium is noted as a key pathogen in periodontal disease, a common comorbidity in endometriosis. These findings suggest a role for the oral, stool and, vaginal microbiome in endometriosis, and present potential for microbial-based treatments and the design of a diagnostic swab.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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
- 18
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
- 39
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
|---|---|---|
| Bacteria | ||
| Butyricicoccus | ||
| Eubacteriales | ||
| Lachnospira | ||
| Peptococcaceae | ||
| Victivallaceae | ||
| Streptococcaceae bacterium RF32 | ||
| Enterococcaceae bacterium RF39 |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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, WikiWorks
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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, WikiWorks
Experiment 7
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
Subjects
- 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,vagina
- 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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Experiment 8
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Experiment 9
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Experiment 10
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Experiment 11
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
Experiment 12
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
Differences from previous experiment shown
Subjects
- 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,vagina
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-28
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 |
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