Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion
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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
- United States of America
- 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
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Antibiotics (Abx) mice and Recolonized mice (Abx + R)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of male mice given regular water.
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
- 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
- 2.0
Signature 1
Source: Figure 4B
Description: Differentially abundant taxa (species level) that showed significant differences in relative abundance of bacterial communities in control (blue), Abx (red) and Abx + R (green) cohorts as identified by linear discriminant analysis (LDA) assessed by effect size analysis (LefSe) algorithm.
Abundance in Group 1: increased abundance in Control mice
Revision editor(s): Aleru Divine, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control mice and Antibiotics (Abx) mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recolonized mice (Abx + R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Differentially abundant taxa (species level) that showed significant differences in relative abundance of bacterial communities in control (blue), Abx (red) and Abx + R (green) cohorts as identified by linear discriminant analysis (LDA) assessed by effect size analysis (LefSe) algorithm.
Abundance in Group 1: increased abundance in Recolonized mice (Abx + R)
Revision editor(s): Aleru Divine, WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control mice and Recolonized mice (Abx + R)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotics (Abx) mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of male mice given a cocktail of non-absorbable broad-spectrum antibiotics (Abx) in the drinking water for two weeks before injection with insulin or saline.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Differentially abundant taxa (species level) that showed significant differences in relative abundance of bacterial communities in control (blue), Abx (red) and Abx + R (green) cohorts as identified by linear discriminant analysis (LDA) assessed by effect size analysis (LefSe) algorithm.
Abundance in Group 1: increased abundance in Antibiotics (Abx) mice
| NCBI | Quality Control | Links |
|---|---|---|
| Shigella boydii | ||
| Shigella flexneri | ||
| Shigella dysenteriae | ||
| Shigella sonnei | ||
| Escherichia |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to stress response to abiotic stress,response to biotic stress,Response to stress,response to stress
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recolonized mice (Abx + R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 5A
Description: Differentially abundant taxa associated with stress response (species level) that showed significance in relative abundance between control and Abx + R cohorts, as identified by LefSe.
Abundance in Group 1: increased abundance in Recolonized mice (Abx + R)
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure 5A
Description: Differentially abundant taxa associated with stress response (species level) that showed significance in relative abundance between control and Abx + R cohorts, as identified by LefSe.
Abundance in Group 1: decreased abundance in Recolonized mice (Abx + R)
Revision editor(s): Aleru Divine, WikiWorks
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotics (Abx) mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of male mice given a cocktail of non-absorbable broad-spectrum antibiotics (Abx) in the drinking water for two weeks before injection with insulin or saline.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts
Abundance in Group 1: increased abundance in Antibiotics (Abx) mice
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Shigella boydii | ||
| Shigella dysenteriae | ||
| Shigella flexneri | ||
| Shigella sonnei | ||
| Staphylococcus aureus |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Table S1
Description: Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts
Abundance in Group 1: decreased abundance in Antibiotics (Abx) mice
Revision editor(s): Aleru Divine, WikiWorks
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recolonized mice (Abx + R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts
Abundance in Group 1: increased abundance in Recolonized mice (Abx + R)
| NCBI | Quality Control | Links |
|---|---|---|
| Cupriavidus metallidurans | ||
| Adlercreutzia caecimuris | ||
| Agathobacter rectalis |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Table S1
Description: Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts
Abundance in Group 1: decreased abundance in Recolonized mice (Abx + R)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus sp. G3(2012) | ||
| Christensenella | ||
| Enterocloster clostridioformis | ||
| Lachnospiraceae bacterium A4 | ||
| Lachnospiraceae bacterium 10-1 | ||
| Bacteroides xylanisolvens |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Antibiotics (Abx) mice
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts
Abundance in Group 1: increased abundance in Recolonized mice (Abx + R)
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Table S1
Description: Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts
Abundance in Group 1: decreased abundance in Recolonized mice (Abx + R)
| NCBI | Quality Control | Links |
|---|---|---|
| Shigella flexneri | ||
| Shigella sonnei | ||
| Shigella boydii | ||
| Shigella dysenteriae | ||
| Escherichia coli |
Revision editor(s): Aleru Divine, WikiWorks
