Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep
-
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.
- Ovis aries
- 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
- Myostatin-related muscle hypertrophy MSLHP,muscle hypertrophy,myostatin-related muscle hypertrophy,Myostatin-related muscle hypertrophy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- WTF(Wild-type female)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GEF(Gene-edited female)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- GEF refers to the Myostatin edited female sheep(MSTN-edited female sheep).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 2C, 2E and 2F
Description: Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF).
Abundance in Group 1: increased abundance in GEF(Gene-edited female)
Revision editor(s): KateRasheed, MyleeeA
Signature 2
Source: Figure 2C, 2E and 2F
Description: Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF).
Abundance in Group 1: decreased abundance in GEF(Gene-edited female)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Bacteroidia bacterium | ||
| Bacteroidota | ||
| Phocaeicola vulgatus |
Revision editor(s): KateRasheed, MyleeeA
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- unchanged
- 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 2G
Description: Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF) using LEfSe.
Abundance in Group 1: increased abundance in GEF(Gene-edited female)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Clostridiales bacterium | ||
| Eubacteriales |
Revision editor(s): KateRasheed, MyleeeA
Signature 2
Source: Figure 2G
Description: Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF) using LEfSe.
Abundance in Group 1: decreased abundance in GEF(Gene-edited female)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Prevotellaceae |
Revision editor(s): KateRasheed, MyleeeA
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- WTM(Wild-type male)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GEM(Gene-edited male)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- GEM refers to the Myostatin edited male sheep(MSTN-edited male sheep).
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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: Supplementary Figure 2C, Supplementary Figure 2D and Supplementary Figure 2F
Description: Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM).
Abundance in Group 1: increased abundance in GEM(Gene-edited male)
Revision editor(s): KateRasheed, MyleeeA
Signature 2
Source: Supplementary Figure 2C, Supplementary Figure 2D and Supplementary Figure 2F
Description: Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM).
Abundance in Group 1: decreased abundance in GEM(Gene-edited male)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Bacteroidia bacterium | ||
| Bacteroidota | ||
| Phocaeicola vulgatus |
Revision editor(s): KateRasheed, MyleeeA
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- decreased
- 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: Supplementary Figure 2G
Description: Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM) using LEfSe.
Abundance in Group 1: increased abundance in GEM(Gene-edited male)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Clostridiales bacterium | ||
| Eubacteriales |
Revision editor(s): KateRasheed, MyleeeA
Signature 2
Source: Supplementary Figure 2G
Description: Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM) using LEfSe.
Abundance in Group 1: decreased abundance in GEM(Gene-edited male)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Prevotellaceae |
Revision editor(s): KateRasheed, MyleeeA
