Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice
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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 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Transplant outcome measurement Transplant outcome measurement,transplant outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice transplanted from the healthy controls on Day 14
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 14
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 14 was given 100 µl of the fecal microbiota suspension from the PCOS patients.
- 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
- 3
Alpha Diversity
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig. 2D - 2E
Description: Results of LEfSe analysis and Cladogram showing bacterial taxa whose abundance in the gut significantly differed between D14-P and D14-H (upper and left).
Abundance in Group 1: increased abundance in Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 14
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Akkermansiaceae | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Oscillospiraceae | ||
| Verrucomicrobiales | ||
| Verrucomicrobiia | ||
| Verrucomicrobiota |
Revision editor(s): PreciousChijioke
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice transplanted from the healthy controls on Day 28
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 28
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 28 was given 100 µl of the fecal microbiota suspension from the PCOS patients.
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig. 2D - 2E
Description: Results of LEfSe analysis and Cladogram showing bacterial taxa whose abundance in the gut significantly differed between D28-H and D28-P (lower and right).
Abundance in Group 1: increased abundance in Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 28
| NCBI | Quality Control | Links |
|---|---|---|
| Lawsonibacter | ||
| Rikenellaceae | ||
| Phocaeicola_A_858004Phocaeicola_A_858004 | ||
| Mediterraneibacter_A_155507Mediterraneibacter_A_155507 | ||
| Oscillospiraceae_88309Oscillospiraceae_88309 |
Revision editor(s): PreciousChijioke
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Insulin resistance Drug resistance to insulin (disorder),Insulin resistance,insulin resistance
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low HOMAIR (insulin resistance index) of colonized GF mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High HOMAIR (insulin resistance index) of colonized GF mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The High HOMA-IR (insulin resistance index) of colonized GF mice.
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor HOMAIR, insulin resistance index.
Abundance in Group 1: increased abundance in High HOMAIR (insulin resistance index) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Scatocola | ||
| Catenibacillus | ||
| Clostridium_AClostridium_A | ||
| Mediterranibacter_A_155507Mediterranibacter_A_155507 |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor HOMAIR, insulin resistance index.
Abundance in Group 1: decreased abundance in High HOMAIR (insulin resistance index) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium_AQClostridium_AQ | ||
| Hungatella_A_128155Hungatella_A_128155 | ||
| Klebsiella_724518Klebsiella_724518 |
Revision editor(s): PreciousChijioke
Experiment 5
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 T (testosterone) of colonized GF mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High T (testosterone) of colonized GF mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The High T (testosterone) of colonized GF mice.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor T, testosterone.
Abundance in Group 1: increased abundance in High T (testosterone) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Catenibacillus | ||
| Massiliimalia_59888Massiliimalia_59888 |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor T, testosterone.
Abundance in Group 1: decreased abundance in High T (testosterone) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Negativibacillus | ||
| Clostridium_AQClostridium_AQ | ||
| Fusobacterium_AFusobacterium_A | ||
| Parabacteroides_B_862066Parabacteroides_B_862066 |
Revision editor(s): PreciousChijioke
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Increased body weight Increased body weight,Weight gain,increased body weight
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor SF/Wt, subcutaneous fat weight/body weight.
Abundance in Group 1: increased abundance in High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Massiliimalia_59888Massiliimalia_59888 | ||
| Clostridium_AClostridium_A |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor SF/Wt, subcutaneous fat weight/body weight.
Abundance in Group 1: decreased abundance in High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| UBA11471UBA11471 | ||
| Desulfovibrio_R_446353Desulfovibrio_R_446353 | ||
| Bacteroides_HBacteroides_H | ||
| Clostridium_AQClostridium_AQ | ||
| UMGS1071UMGS1071 |
Revision editor(s): PreciousChijioke
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
- Low TG (triglycerides) of colonized GF mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High TG (triglycerides) of colonized GF mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The High TG (triglycerides) of colonized GF mice.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TG, triglycerides.
Abundance in Group 1: increased abundance in High TG (triglycerides) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Bilophila | ||
| Butyricimonas | ||
| Candidatus Scatocola | ||
| Dysosmobacter | ||
| Extibacter | ||
| Alistipes_A_871400Alistipes_A_871400 | ||
| Phocaeicola_A_858004Phocaeicola_A_858004 |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TG, triglycerides.
Abundance in Group 1: decreased abundance in High TG (triglycerides) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillus | ||
| Romboutsia_BRomboutsia_B | ||
| Clostridium_AQClostridium_AQ |
Revision editor(s): PreciousChijioke
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Low density lipoprotein cholesterol measurement LDL measurement,Low density lipoprotein cholesterol measurement,low density lipoprotein cholesterol measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Decreasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Increasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Increasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor LDL-C; low-density lipoprotein cholesterol.
Abundance in Group 1: increased abundance in Increasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| RUG762RUG762 |
Revision editor(s): PreciousChijioke
Experiment 9
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
- Low TC (total cholesterol) of colonized GF mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High TC (total cholesterol) of colonized GF mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The High TC (total cholesterol) of colonized GF mice.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TC, total cholesterol.
Abundance in Group 1: increased abundance in High TC (total cholesterol) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Parasutterella |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 5
Description: Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TC, total cholesterol.
Abundance in Group 1: decreased abundance in High TC (total cholesterol) of colonized GF mice
| NCBI | Quality Control | Links |
|---|---|---|
| Hungatella sp. UBA3402 | ||
| Bacteroides_HBacteroides_H | ||
| Desulfovibrio_R_446353Desulfovibrio_R_446353 |
Revision editor(s): PreciousChijioke
