Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot 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
Curated date: 2021/08/11
Curator: Samara.Khan
Revision editor(s): Folakunmi, Peace Sandy, WikiWorks, Samara.Khan
Subjects
- Location of subjects
- China
- 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
- Cervical cavity Canal of the cervix,Cavity of cervix,Cervical canal,Cervical canal of uterus,Endocervical,Endocervical canal,Endocervix,Lumen of cervix of uterus,Cervical cavity,cervical cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Endometriosis , Adenomyosis 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,uterine corpus adenomyosis,Adenomyosis,adenomyosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Endometriosis patients (EM) and Patients without endometriosis(Control-CT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Endometriosis/ adenomyosis patients (AMEM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All participants were diagnosed with adenomyosis accompanied with endometriosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery
- Group 0 sample size Number of subjects in the control (unexposed) group
- 92
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotic use within 30 days
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of 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: within results text(under "Microbiota composition of different diseases" ,paragraph 5, lines 4-7), figure 6
Description: The following taxa were increased in patients with endometriosis and adenomyosis compared to those with just endometriosis, as well as those without endometriosis (control).
Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients (AMEM)
NCBI | Quality Control | Links |
---|---|---|
Atopobium | ||
Campylobacter | ||
Campylobacteraceae | ||
Coriobacteriaceae | ||
Escherichia/Shigella sp. | ||
Ezakiella | ||
Faecalibacterium |
Revision editor(s): Samara.Khan, Folakunmi
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients without endometriosis (CT), patients with only endometriosis(EM)) and patients with only adenomysis(AM)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 120
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of 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: within results text(under "Microbiota composition of different diseases" ,paragraph 5, lines 4-7), figure 6
Description: The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those without endometriosis, patients with only endometriosis and patients with only adenomysis.
Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients (AMEM)
NCBI | Quality Control | Links |
---|---|---|
Campylobacteraceae | ||
Coriobacteriaceae |
Revision editor(s): Samara.Khan, Folakunmi
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adenomysis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All participants were diagnosed with endometriosis and/or adenomyosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of 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: within results text (under "Microbiota composition of different diseases" ,paragraph 5, lines 4-7), figure 6
Description: The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those with only adenomyosis.
Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients (AMEM)
NCBI | Quality Control | Links |
---|---|---|
Atopobium | ||
Campylobacter | ||
Ezakiella | ||
Faecalibacterium |
Revision editor(s): Folakunmi