Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine
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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
- Response to diet Response to diet,response to diet
- 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
- HFD (High fat diet)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female Wistar rats of 21 days fed a high-fat chow, energy%: 60% from fat, 20% from carbohydrates and 20% from protein, 5.24 kcal/g (Research Diets, D12492).
- 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
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- 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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 5D
Description: The abundance of Spirochaetaceae at the family level.
Abundance in Group 1: decreased abundance in HFD (High fat diet)
NCBI | Quality Control | Links |
---|---|---|
Spirochaetaceae |
Revision editor(s): Anne-mariesharp
Experiment 2
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- DHT (Dihydrotestosterone)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female Wistar rats of 21 days fed with standard chow, energy%: 10.3% from fat, 65.5% from carbohydrate and 24.2% from protein, 3.52kcal/g (Shanghai SLAC Laboratory Animal) and implanted subcutaneously with slow-release Dihydrotestosterone (15 mg, 75-day release) silicone tubes at 21 days old to induce Polycystic ovary syndrome
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
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: Figure 5D
Description: The abundance of Spirochaetaceae at the family level.
Abundance in Group 1: decreased abundance in DHT (Dihydrotestosterone)
NCBI | Quality Control | Links |
---|---|---|
Spirochaetaceae |
Revision editor(s): Anne-mariesharp
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- DHT (Dihydrotestosterone) + Berberine
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DHT-induced PCOS rats treated with Berberine daily, starting 7 weeks after DHT implantation
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Figure 5D
Description: The abundance of Spirochaetaceae at the family level.
Abundance in Group 1: decreased abundance in DHT (Dihydrotestosterone) + Berberine
NCBI | Quality Control | Links |
---|---|---|
Spirochaetaceae |
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to diet Response to diet,response to diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HFD (High fat diet)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female Wistar rats of 21 days fed a high-fat chow, energy%: 60% from fat, 20% from carbohydrates and 20% from protein, 5.24 kcal/g (Research Diets, D12492).
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 6A, Supplementary figure 2A
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: increased abundance in HFD (High fat diet)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Ruminococcaceae bacterium UCG-005 | ||
Ruminococcus_1Ruminococcus_1 |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 6A, Supplementary figure 2A
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: decreased abundance in HFD (High fat diet)
NCBI | Quality Control | Links |
---|---|---|
Prevotellaceae_Ga6A1_groupPrevotellaceae_Ga6A1_group | ||
Prevotella_9Prevotella_9 | ||
Treponema_2Treponema_2 |
Revision editor(s): Anne-mariesharp
Experiment 5
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- DHT (Dihydrotestosterone)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female Wistar rats of 21 days fed with standard chow, energy%: 10.3% from fat, 65.5% from carbohydrate and 24.2% from protein, 3.52kcal/g (Shanghai SLAC Laboratory Animal) and implanted subcutaneously with slow-release Dihydrotestosterone (15 mg, 75-day release) silicone tubes at 21 days old to induce Polycystic ovary syndrome
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: Figure 6B, Supplementary figure 2B
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: increased abundance in DHT (Dihydrotestosterone)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Prevotella_9Prevotella_9 |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Supplementary figure 2B
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: decreased abundance in DHT (Dihydrotestosterone)
NCBI | Quality Control | Links |
---|---|---|
Prevotellaceae_Ga6A1_groupPrevotellaceae_Ga6A1_group |
Revision editor(s): Anne-mariesharp
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- DHT (Dihydrotestosterone) + Diane-35
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DHT-induced PCOS rats treated with Diane-35 daily, starting 7 weeks after DHT implantation
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: Supplementary Figure 2C
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: increased abundance in DHT (Dihydrotestosterone) + Diane-35
NCBI | Quality Control | Links |
---|---|---|
Ruminococcaceae_UCG-013Ruminococcaceae_UCG-013 |
Revision editor(s): Amaanarif, Anne-mariesharp
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- DHT (Dihydrotestosterone) + Probiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DHT-induced PCOS rats treated with Probiotics daily, starting 7 weeks after DHT implantation
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: Supplementary Figure 2D
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: decreased abundance in DHT (Dihydrotestosterone) + Probiotics
NCBI | Quality Control | Links |
---|---|---|
Prevotellaceae_Ga6A1_groupPrevotellaceae_Ga6A1_group |
Revision editor(s): Amaanarif, Anne-mariesharp
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- DHT (Dihydrotestosterone) + Berberine
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DHT-induced PCOS rats treated with Berberine daily, starting 7 weeks after DHT implantation
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Figure 6E, Supplementary Figure 2E
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: increased abundance in DHT (Dihydrotestosterone) + Berberine
NCBI | Quality Control | Links |
---|---|---|
Blautia | ||
Phascolarctobacterium | ||
Thomasclavelia | ||
Prevotellaceae_NK3B31_groupPrevotellaceae_NK3B31_group |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 6E, Supplementary Figure 2E
Description: Different fecal microbiota in rats at the genus level
Abundance in Group 1: decreased abundance in DHT (Dihydrotestosterone) + Berberine
Revision editor(s): Anne-mariesharp