Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome
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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.
- Rattus norvegicus
- 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
- Phosphate buffer saline (PBS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dehydroepiandrosterone (DHEA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were injected subcutaneously with DHEA (6 mg/100 g bodyweight) daily for 35 days to induce polycystic ovary syndrome (PCOS).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
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
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Additional file 1: Figure S1d & e
Description: Cladogram and Linear Discriminant Analysis (LDA) score bar plot of differentially abundant taxa enriched in the phosphate buffer saline (PBS) group.
Abundance in Group 1: decreased abundance in Dehydroepiandrosterone (DHEA)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidimicrobiia | ||
| Actinomycetota | ||
| Anaerofustis | ||
| Clostridium | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Erysipelotrichia | ||
| Turicibacter | ||
| Clostridiaceae 1Clostridiaceae 1 |
Revision editor(s): Victoria
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- t-Phosphate buffer saline (t-PBS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- t-Dehydroepiandrosterone (t-DHEA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal microbiota transplant (FMT) recipient rats from the Dehydroepiandrosterone (DHEA) group.
Lab analysis
Statistical Analysis
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 3d and e
Description: Cladogram and bar plot of LEfSe analysis showed taxa contribution to group separation. Taxa with an LDA score > 2 were displayed.
Abundance in Group 1: decreased abundance in t-Dehydroepiandrosterone (t-DHEA)
Revision editor(s): Victoria
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Glucose tolerance test Glucose tolerance test,glucose tolerance test
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low glucose tolerance
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High glucose tolerance
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high glucose tolerance.
- 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 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High glucose tolerance
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus |
Revision editor(s): Victoria
Signature 2
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: decreased abundance in High glucose tolerance
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): Victoria
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fasting blood glucose measurement fasting blood glucose level,fasting glucose-related traits,fasting plasma glucose,Fasting blood glucose measurement,fasting blood glucose measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low fasting blood glucose level
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High fasting blood glucose level
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high fasting blood glucose levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High fasting blood glucose level
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroplasma | ||
| Lactobacillus | ||
| Mucispirillum |
Revision editor(s): Victoria
Signature 2
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: decreased abundance in High fasting blood glucose level
| NCBI | Quality Control | Links |
|---|---|---|
| Bilophila | ||
| Sporobacter | ||
| Sutterella | ||
| Bacteroides | ||
| Erysipelotrichaceae incertae sedis |
Revision editor(s): Victoria
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hormone measurement Hormone measurement,hormone measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Luteinising hormone/ Follicle-stimulating hormone
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Luteinising hormone/ Follicle-stimulating hormone
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high Luteinising hormone/ Follicle-stimulating hormone levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: decreased abundance in High Luteinising hormone/ Follicle-stimulating hormone
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium XVIIIClostridium XVIII | ||
| Romboutsia |
Revision editor(s): Victoria
Experiment 6
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
- Low Follicle-stimulating hormone
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Follicle-stimulating hormone
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high Follicle-stimulating hormone levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High Follicle-stimulating hormone
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Rothia | ||
| Olsenella | ||
| Clostridium |
Revision editor(s): Victoria
Experiment 7
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
- Low Luteinising hormone
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Luteinising hormone
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high Luteinising hormone levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High Luteinising hormone
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Rothia |
Revision editor(s): Victoria
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Free androgen index Free androgen index,free androgen index
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Free androgen index
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Free androgen index
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high Free androgen index levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: decreased abundance in High Free androgen index
| NCBI | Quality Control | Links |
|---|---|---|
| Olsenella |
Revision editor(s): Victoria
Experiment 9
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
- Low Sex hormone-binding globulin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Sex hormone-binding globulin
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high Sex hormone-binding globulin.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High Sex hormone-binding globulin
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae incertae sedis | ||
| Bilophila |
Revision editor(s): Victoria
Signature 2
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: decreased abundance in High Sex hormone-binding globulin
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Rothia |
Revision editor(s): Victoria
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Testosterone measurement testosterone level,testosterone levels,Testosterone measurement,testosterone measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Total testosterone
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Total testosterone
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high Total testosterone levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High Total testosterone
| NCBI | Quality Control | Links |
|---|---|---|
| Bilophila |
Revision editor(s): Victoria
Signature 2
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: decreased abundance in High Total testosterone
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroplasma | ||
| Olsenella | ||
| Turicibacter | ||
| Clostridium |
Revision editor(s): Victoria
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body weight weight,Body weight,body weight
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low body weight
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High body weight
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group had high body weight.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3h
Description: Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.
Abundance in Group 1: increased abundance in High body weight
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus |
Revision editor(s): Victoria
