Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia
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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
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Polycystic ovary syndrome Cystic disease of ovaries,hyperandrogenemia,Multicystic ovaries,multicystic ovaries,Ovarian Degeneration, Sclerocystic,Ovarian Syndrome, Polycystic,Ovarian Syndromes, Polycystic,Ovaries, Sclerocystic,Ovary Syndrome, Polycystic,Ovary, Sclerocystic,PCO - Polycystic ovaries,Pco1,PCOD - Polycystic ovarian disease,PCOS,Pcos,PCOS - Polycystic ovarian syndrome,PCOS1,Polycystic ovarian disease,polycystic ovarian disease,Polycystic ovarian syndrome,Polycystic ovaries,polycystic ovaries,Polycystic ovaries (disorder),polycystic ovary,polycystic ovary syndrome,polycystic ovary syndrome 1,Sclerocystic Ovarian Degeneration,Sclerocystic Ovaries,Sclerocystic Ovary,Sclerocystic Ovary Syndrome,Stein Leventhal Syndrome,Stein-Leventhal synd.,Stein-Leventhal Syndrome,Stein-Leventhal syndrome,Syndrome, Polycystic Ovary,Syndrome, Stein-Leventhal,Polycystic ovary syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polycystic ovary syndrome (PCOS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 3A
Description: LEfSe and Cladogram analyses of significantly different classification units between Control and PCOS.
Abundance in Group 1: increased abundance in Polycystic ovary syndrome (PCOS)
Revision editor(s): Victoria
Signature 2
Source: Figure 3A
Description: LEfSe and Cladogram analyses of significantly different classification units between Control and PCOS.
Abundance in Group 1: decreased abundance in Polycystic ovary syndrome (PCOS)
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichaceae | ||
| Pseudomonadales | ||
| Pseudomonas | ||
| Pseudomonadaceae | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Victoria
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polycystic ovary syndrome & Dyslipidemia (PCOS.D)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Dyslipidemia and Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.
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
Signature 1
Source: Figure 3B
Description: LEfSe and Cladogram analyses of significantly different classification units between Control and PCOS.D.
Abundance in Group 1: increased abundance in Polycystic ovary syndrome & Dyslipidemia (PCOS.D)
Revision editor(s): Victoria
Signature 2
Source: Figure 3B
Description: LEfSe and Cladogram analyses of significantly different classification units between Control and PCOS.D.
Abundance in Group 1: decreased abundance in Polycystic ovary syndrome & Dyslipidemia (PCOS.D)
Revision editor(s): Victoria
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polycystic ovary syndrome (PCOS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polycystic ovary syndrome & Dyslipidemia(PCOS.D)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
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
Signature 1
Source: Figure 3C
Description: LEfSe and Cladogram analyses of significantly different classification units between PCOS and PCOS.D.
Abundance in Group 1: increased abundance in Polycystic ovary syndrome & Dyslipidemia(PCOS.D)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Eubacteriales | ||
| Clostridiaceae | ||
| swine fecal bacterium SD-Pec10 | ||
| Mitsuokella |
Revision editor(s): Victoria
Signature 2
Source: Figure 3C
Description: LEfSe and Cladogram analyses of significantly different classification units between PCOS and PCOS.D.
Abundance in Group 1: decreased abundance in Polycystic ovary syndrome & Dyslipidemia(PCOS.D)
Revision editor(s): Victoria
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Aspartate aminotransferase measurement Aspartate transaminase measurement,Aspartate aminotransferase measurement,aspartate aminotransferase measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Aspartate aminotransferase__AST (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Aspartate aminotransferase__AST (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High levels of Aspartate aminotransferase(AST).
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Aspartate aminotransferase__AST (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Victoria
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- LDL cholesterol cholesterol, LDL,High-density lipoprotein cholesterol,High-density lipoproteins,LDL lipoproteins,lipoproteins, LDL,LDL cholesterol,lDL cholesterol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low-density lipoprotein cholesterol__LDL-C (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low-density lipoprotein cholesterol__LDL-C (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Low-density lipoprotein cholesterol (LDL-C), short-chain fatty acids(SCFAs).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in Low-density lipoprotein cholesterol__LDL-C (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter |
Revision editor(s): Victoria
Signature 2
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Low-density lipoprotein cholesterol__LDL-C (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas | ||
| Holdemanella | ||
| Parasutterella |
Revision editor(s): Victoria
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HDL cholesterol alpha Lipoprotein Cholesterol,alpha Lipoproteins,alpha-1 Lipoprotein,alpha-Lipoprotein Cholesterol,alpha-Lipoproteins,Cholesterol, alpha-Lipoprotein,Cholesterol, HDL,Cholesterol, HDL2,Cholesterol, HDL3,HDL Lipoproteins,HDL(2) Cholesterol,HDL(3) Cholesterol,HDL2 Cholesterol,HDL3 Cholesterol,Heavy Lipoproteins,High Density Lipoprotein Cholesterol,High Density Lipoproteins,high-density lipoprotein cholesterol,High-Density Lipoproteins,Lipoproteins, HDL,Lipoproteins, Heavy,Lipoproteins, High-Density,HDL cholesterol,hDL cholesterol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-density lipoprotein cholesterol__HDL-C (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-density lipoprotein cholesterol__HDL-C (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of High-density lipoprotein cholesterol (HDL-C).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in High-density lipoprotein cholesterol__HDL-C (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Achromobacter |
Revision editor(s): Victoria
Signature 2
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in High-density lipoprotein cholesterol__HDL-C (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Parasutterella |
Revision editor(s): Victoria
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Triglyceride measurement triglyceride levels,Triglyceride measurement,triglyceride measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Triglyceride__TG (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Triglyceride__TG (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Triglyceride (TG).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Triglyceride__TG (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Ruminococcus |
Revision editor(s): Victoria
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Total cholesterol measurement cholesterol, total,total cholesterol levels,Total cholesterol measurement,total cholesterol measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Total cholesterol__TC (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Total cholesterol__TC (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Triglyceride (TC).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in Total cholesterol__TC (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Achromobacter |
Revision editor(s): Victoria
Signature 2
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Total cholesterol__TC (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Holdemanella | ||
| Parasutterella |
Revision editor(s): Victoria
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HOMA-IR homeostasis model assessment insulin resistance,HOMA-IR,hOMA-IR
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Homeostatic model assessment for insulin resistance__HOMA-IR (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Homeostatic model assessment for insulin resistance__HOMA-IR (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Homeostatic model assessment for insulin resistance (HOMA-IR).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Homeostatic model assessment for insulin resistance__HOMA-IR (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides |
Revision editor(s): Victoria
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hyperproinsulinemia hyperproinsulinemia,Hyperproinsulinemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Fasting plasma insulin__FINS (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fasting plasma insulin__FINS (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Fasting plasma insulin (FINS).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Fasting plasma insulin__FINS (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides |
Revision editor(s): Victoria
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Dehydroepiandrosterone measurement DHEA measurement,Dehydroepiandrosterone measurement,dehydroepiandrosterone measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Dehydroepiandrosterone__DHEA (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dehydroepiandrosterone__DHEA (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Dehydroepiandrosterone (DHEA).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in Dehydroepiandrosterone__DHEA (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia | ||
| Blautia | ||
| Prevotella 9Prevotella 9 |
Revision editor(s): Victoria
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sex hormone-binding globulin measurement SHBG level,SHBG levels,Sex hormone-binding globulin measurement,sex hormone-binding globulin measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sex hormone-binding globulin__SHBG (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sex hormone-binding globulin__SHBG (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Sex hormone-binding globulin (SHBG).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in Sex hormone-binding globulin__SHBG (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Bifidobacterium |
Revision editor(s): Victoria
Signature 2
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Sex hormone-binding globulin__SHBG (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Ralstonia |
Revision editor(s): Victoria
Experiment 13
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hyperpituitarism Hyperpituitarism,hyperpituitarism
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Luteinizing hormone/Follicle-stimulating hormone (LH/FSH).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Parabacteroides | ||
| Prevotella 9Prevotella 9 |
Revision editor(s): Victoria
Signature 2
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Victoria
Experiment 14
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Follicle stimulating hormone measurement follicle stimulating hormone level,follicle stimulating hormone levels,FSH level,FSH levels,Follicle stimulating hormone measurement,follicle stimulating hormone measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Follicle-stimulating hormone__FSH (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Follicle-stimulating hormone__FSH (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Follicle-stimulating hormone (FSH).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Follicle-stimulating hormone__FSH (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Clostridium |
Revision editor(s): Victoria
Experiment 15
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Luteinizing hormone measurement LH measurement,Luteinizing hormone measurement,luteinizing hormone measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Luteinizing hormone__LH (Decreased)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Luteinizing hormone__LH (Increased)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased levels of Luteinizing hormone (LH).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: increased abundance in Luteinizing hormone__LH (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Parabacteroides | ||
| Ruminococcus | ||
| Prevotella 9Prevotella 9 |
Revision editor(s): Victoria
Signature 2
Source: Figure 5A
Description: Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.
Abundance in Group 1: decreased abundance in Luteinizing hormone__LH (Increased)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Victoria
