Effect of metformin on metabolic improvement and gut microbiota
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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
- South Korea
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-Fat-Diet to Normal Diet group (HFD-ND) and High-Fat-Diet + Metformin group (HFD-Met)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Fat-Diet group (HFD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of mice receiving HFD without metformin treatment (HFD group).
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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
- 4.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Source: Figure 4E
Description: Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.
Abundance in Group 1: increased abundance in High-Fat-Diet group (HFD)
Revision editor(s): Aleru Divine, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-Fat-Diet group (HFD) and High-Fat-Diet + Metformin group (HFD-Met)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Fat-Diet to Normal Diet group (HFD-ND)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of mice that received a dietary change from a High-Fat-Diet to Normal Diet group (HFD-ND).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.
Abundance in Group 1: increased abundance in High-Fat-Diet to Normal Diet group (HFD-ND)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Akkermansia muciniphila | ||
| Bacteroidaceae | ||
| Clostridium | ||
| Eubacteriales Family XIII. Incertae Sedis | ||
| Thomasclavelia cocleata | ||
| Verrucomicrobiaceae | ||
| unclassified Bacteroides |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to metformin Response to metformin,response to metformin
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-Fat-Diet to Normal Diet group (HFD-ND) and High-Fat-Diet group (HFD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Fat-Diet + Metformin group (HFD-Met)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of mice that had Metformin (300 mg/kg of body weight 1,1-dimethylbiguanide hydrochloride; Sigma-Aldrich) administered every day during the HFD for 10 weeks (HFD-Met group).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.
Abundance in Group 1: increased abundance in High-Fat-Diet + Metformin group (HFD-Met)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Rikenellaceae |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Diet group (ND)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal Diet + Met group(ND-Met)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of mice receiving Normal Diet (ND) with metformin treatment (ND-Met).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4F
Description: Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.
Abundance in Group 1: increased abundance in Normal Diet + Met group(ND-Met)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Rikenellaceae | ||
| Flavonifractor plautii | ||
| Clostridium | ||
| unclassified Oscillospiraceae | ||
| Verrucomicrobiaceae | ||
| Akkermansia muciniphila | ||
| Akkermansia |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure 4F
Description: Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.
Abundance in Group 1: decreased abundance in Normal Diet + Met group(ND-Met)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners | ||
| Lactobacillus | ||
| Lactobacillaceae |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of female mice on High-Fat-Diet (HFD).
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.0
Signature 1
Source: Figure 5A
Description: Differences in the gut microbiota between male and female mice in the HFD group.
Abundance in Group 1: increased abundance in Female mice
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| unclassified Bacteroides | ||
| Bacteroidota | ||
| Bacteroidaceae |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure 5A
Description: Differences in the gut microbiota between male and female mice in the HFD group.
Abundance in Group 1: decreased abundance in Female mice
Revision editor(s): Aleru Divine, WikiWorks
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to metformin Response to metformin,response to metformin
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of female mice that were administered Metformin (300 mg/kg of body weight 1,1-dimethylbiguanide hydrochloride; Sigma-Aldrich) every day during the HFD for 10 weeks (HFD-Met group).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5B
Description: Differences in the gut microbiota between male and female mice in the HFD-Met group.
Abundance in Group 1: increased abundance in Female mice
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidia | ||
| Lactobacillaceae | ||
| Bacteroides | ||
| Clostridium | ||
| Flavonifractor plautii |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure 5B
Description: Differences in the gut microbiota between male and female mice in the HFD-Met group.
Abundance in Group 1: decreased abundance in Female mice
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Coprobacillus |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of female mice that received a dietary change from a High-Fat-Diet to Normal Diet group (HFD-ND).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5C
Description: Differences in the gut microbiota between male and female mice in the HFD-ND group.
Abundance in Group 1: decreased abundance in Female mice
| NCBI | Quality Control | Links |
|---|---|---|
| Mollicutes | ||
| Mycoplasmatota |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 8
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of female mice receiving Normal Diet (ND).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5D
Description: Differences in the gut microbiota between male and female mice in the ND group.
Abundance in Group 1: increased abundance in Female mice
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Erysipelotrichaceae | ||
| Porphyromonadaceae | ||
| Parabacteroides |
Revision editor(s): Aleru Divine, WikiWorks
