Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells
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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
Curated date: 2022/11/21
Curator: Fatima
Revision editor(s): Lwaldron, Fatima, Peace Sandy, Joan Chuks, Victoria
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- 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 ketogenic diet Response to ketogenic diet,response to ketogenic diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Overweight/Obese Men on Baseline Diet (BD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overweight/Obese Men on Ketogenic Diet (KD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Overweight or class I Obese non-diabetic men who consumed an isocaloric ketogenic diet for 4weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
Signature 1
Source: Figure 1E
Description: Bacterial taxa identified by DESeq2 as differentially abundant in Overweight/class I Obese non-diabetic Men, who consumed an isocaloric ketogenic diet for 4weeks Versus the same Overweight/class I Obese non-diabetic Men on Baseline Diet for 4weeks.
Abundance in Group 1: increased abundance in Overweight/Obese Men on Ketogenic Diet (KD)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Faecalitalea | ||
| Flavonifractor | ||
| Fusobacterium | ||
| Intestinibacter | ||
| Intestinimonas | ||
| Megamonas | ||
| Negativibacillus | ||
| Parasutterella | ||
| Prevotella sp. 1-8 | ||
| Thomasclavelia |
Revision editor(s): Fatima, Lwaldron, Joan Chuks
Signature 2
Source: Figure 1E
Description: Bacterial taxa identified by DESeq2 as differentially abundant in Overweight/class I Obese non-diabetic Men, who consumed an isocaloric ketogenic diet for 4weeks Versus the same Overweight/class I Obese non-diabetic Men on Baseline Diet for 4weeks.
Abundance in Group 1: decreased abundance in Overweight/Obese Men on Ketogenic Diet (KD)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Anaerostipes | ||
| Bifidobacterium | ||
| Dialister | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Streptococcus | ||
| Ruminococcus sp. |
Revision editor(s): Joan Chuks
Experiment 2
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice fed on High-fat Diet (HFD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed on Ketogenic Diet (KD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Wild-type C57BL/6J mice of both sexes, between age 5 - 10 weeks, fed on ketogenic diet for 3 weeks.
- 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
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- Matched on Factors on which subjects have been matched on in a case-control study
- diet
Signature 1
Source: Figure 3G + Figure S4F + Figure 5I
Description: Bacterial taxa identified by DESeq2 as differentially abundant in Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on Ketogenic Diet(KD) Versus the Mice fed on High-Fat Diet (HFD).
Abundance in Group 1: increased abundance in Mice fed on Ketogenic Diet (KD)
Revision editor(s): Joan Chuks
Signature 2
Source: Figure 3G + Figure S4F
Description: Bacterial taxa identified by DESeq2 as differentially abundant in Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on Ketogenic Diet(KD) Versus Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on High-Fat Diet (HFD).
Abundance in Group 1: decreased abundance in Mice fed on Ketogenic Diet (KD)
Revision editor(s): Joan Chuks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice fed on High-fat Diet (HFD-control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed High-fat Diet + Ketone Ester (HFD-KE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- C57BL/6J mice fed on High-fat diet that was supplemented with a synthetic Ketone ester(KE), beta-hydroxybutyrate(bHB).
- 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
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Source: Figure 5I + Figure 5M
Description: Bacterial taxa identified by DESeq2 as differentially abundant in C57BL/6J mice fed on High-fat diet supplemented with Ketone ester(KE), beta-hydroxybutyrate(bHB) Versus Mice fed on only High-Fat Diet (HFD).
Abundance in Group 1: increased abundance in Mice fed High-fat Diet + Ketone Ester (HFD-KE)
| NCBI | Quality Control | Links |
|---|---|---|
| Acetatifactor | ||
| Bacteroides | ||
| Faecalibacterium | ||
| Parabacteroides | ||
| Prevotella |
Revision editor(s): Joan Chuks
Signature 2
Source: Figure 5M
Description: Bacterial taxa identified by DESeq2 as differentially abundant in C57BL/6J mice fed on High-fat diet supplemented with Ketone ester(KE), beta-hydroxybutyrate(bHB) Versus Mice fed on only High-Fat Diet (HFD).
Abundance in Group 1: decreased abundance in Mice fed High-fat Diet + Ketone Ester (HFD-KE)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Collinsella | ||
| Enterococcus | ||
| Escherichia/Shigella sp. | ||
| Lactobacillus | ||
| Streptococcus | ||
| Turicibacter | ||
| Clostridium_sensu_stricto_1Clostridium_sensu_stricto_1 |
Revision editor(s): Joan Chuks
