Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets
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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: 2024/11/27
Curator:
Revision editor(s):
Subjects
- Location of subjects
- China
- 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
- Epilepsy [X]Other epilepsy,[X]Other epilepsy (disorder),EF - Epileptic fit,EP - Epilepsy,Epilectic attack, NOS,EPILEP NEC W/O INTR EPIL,EPILEP NOS W/O INTR EPIL,epilepsy,Epilepsy (disorder),Epilepsy and recurrent seizures,EPILEPSY NEC W INTR EPIL,Epilepsy NOS,Epilepsy NOS (disorder),EPILEPSY NOS W INTR EPIL,Epilepsy, NOS,Epilepsy, unspecified,Epilepsy, unspecified, with intractable epilepsy,Epilepsy, unspecified, without mention of intractable epilepsy,Epileptic,Epileptic attack,Epileptic attack, NOS,Epileptic convulsions,Epileptic convulsions, NOS,Epileptic disorder,Epileptic disorder, NOS,Epileptic fit,Epileptic fits,Epileptic fits, NOS,Epileptic Seizure,Epileptic seizure (finding),Epileptic seizures,Epileptic seizures, NOS,Generalised convulsion,Generalised fit,Generalised seizure,Generalized convulsion,Generalized fit,Generalized seizure,Generalized seizure (finding),Other forms of epilepsy,Other forms of epilepsy (disorder),Other forms of epilepsy and recurrent seizures,Other forms of epilepsy NOS,Other forms of epilepsy NOS (disorder),Other forms of epilepsy, with intractable epilepsy,Other forms of epilepsy, without mention of intractable epilepsy,Seizure disorder,seizure disorder,Seizure disorder (disorder),Epilepsy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-ketogenic diet (KD1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with drug refractory epilepsy (DRE) before ketogenic diet (KD) treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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).
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, Matched on: "gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gender
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 2
Description: Fecal microbiome of KD1 group compared to healthy controls
Abundance in Group 1: increased abundance in
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Source: Figure 2
Description: Fecal microbiome of KD1 group compared to healthy controls
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Oscillospiraceae |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 2
Curated date: 2024/11/27
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-ketogenic diet (KD2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with DRE after KD treatment
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 4E-H
Description: Fecal microbiome of KD2 group compared to healthy controls
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Dialister | ||
| Subdoligranulum | ||
| unclassified Ruminococcus |
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Source: Figure 4A-D
Description: Fecal microbiome of KD2 group compared to healthy controls
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Akkermansia | ||
| Enterococcus |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 3
Curated date: 2024/11/27
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Epilepsy [X]Other epilepsy,[X]Other epilepsy (disorder),EF - Epileptic fit,EP - Epilepsy,Epilectic attack, NOS,EPILEP NEC W/O INTR EPIL,EPILEP NOS W/O INTR EPIL,epilepsy,Epilepsy (disorder),Epilepsy and recurrent seizures,EPILEPSY NEC W INTR EPIL,Epilepsy NOS,Epilepsy NOS (disorder),EPILEPSY NOS W INTR EPIL,Epilepsy, NOS,Epilepsy, unspecified,Epilepsy, unspecified, with intractable epilepsy,Epilepsy, unspecified, without mention of intractable epilepsy,Epileptic,Epileptic attack,Epileptic attack, NOS,Epileptic convulsions,Epileptic convulsions, NOS,Epileptic disorder,Epileptic disorder, NOS,Epileptic fit,Epileptic fits,Epileptic fits, NOS,Epileptic Seizure,Epileptic seizure (finding),Epileptic seizures,Epileptic seizures, NOS,Generalised convulsion,Generalised fit,Generalised seizure,Generalized convulsion,Generalized fit,Generalized seizure,Generalized seizure (finding),Other forms of epilepsy,Other forms of epilepsy (disorder),Other forms of epilepsy and recurrent seizures,Other forms of epilepsy NOS,Other forms of epilepsy NOS (disorder),Other forms of epilepsy, with intractable epilepsy,Other forms of epilepsy, without mention of intractable epilepsy,Seizure disorder,seizure disorder,Seizure disorder (disorder),Epilepsy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-ketogenic diet (KD1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with DRE before KD treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figures 4A-D & 5A-C
Description: Fecal microbiome of KD1 group compared to healthy controls
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Akkermansia | ||
| Bifidobacterium | ||
| Enterococcus | ||
| Bacteroides | ||
| Mycoplasmatota |
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Source: Figures 4E-G & 5E-F
Description: Fecal microbiome of KD1 group compared to healthy controls
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Dialister | ||
| Subdoligranulum | ||
| unclassified Christensenellaceae |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 4
Curated date: 2024/11/28
Curator:
Revision editor(s):
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Metastats
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 5E-F
Description: Comparing difference in fecal microbiome of children with DRE before KD treatment (KD1 group) to healthy controls
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| unclassified Christensenellaceae |
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Source: Figure 5A-C
Description: Comparing difference in fecal microbiome of children with DRE before KD treatment (KD1 group) to healthy controls
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroides | ||
| Mycoplasmatota |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KD2 responders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with DRE who were classified as having seizure reduction frequency greater than or equal to 50% after KD treatment. Samples analyzed from KD2 group.
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Figure 5D-F
Description: Fecal microbiome of KD2 responders compared to healthy controls
Abundance in Group 1: decreased abundance in KD2 responders
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| unclassified Christensenellaceae | ||
| unclassified Ruminococcus |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 6
Curated date: 2024/12/09
Curator:
Revision editor(s):
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
- KD2 nonresponders
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Signature 1
Source: Results Section 3.3 (Text)
Description: Fecal microbiome of KD2 responders compared to KD2 nonresponders
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Eubacterium |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- KD1 without gene mutation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KD2 without gene mutation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with DRE and without gene mutation after KD treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Signature 1
Source: Results Section 3.3 (Text)
Description: Fecal microbiome of KD2 children without gene mutation compared to KD1 children without gene mutation
Abundance in Group 1: increased abundance in KD2 without gene mutation
| NCBI | Quality Control | Links |
|---|---|---|
| Hungatella |
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Source: Results Section 3.3 (Text)
Description: Fecal microbiome of KD1 children with gene mutation compared to KD1 children without gene mutation
Abundance in Group 1: decreased abundance in KD2 without gene mutation
| NCBI | Quality Control | Links |
|---|---|---|
| Dactylosporangium |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 8
Curated date: 2024/12/09
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- KD1 with gene mutation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KD2 with gene mutation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with DRE and gene mutation after KD treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Signature 1
Source: Results Section 3.3 (Text)
Description: Fecal microbiome of KD2 children with gene mutation compared to KD1 children with gene mutation
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides |
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Source: Results Section 3.3 (Text)
Description: Comparing post-KD treatment children with DRE who have positive gene mutation vs those who do not
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Hungatella |
Revision editor(s): Kavyaayala, WikiWorks
