Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Xie G, Zhou Q, Qiu CZ, Dai WK, Wang HP, Li YH, Liao JX, Lu XG, Lin SF, Ye JH, Ma ZY, Wang WJ
Journal
World journal of gastroenterology
Year
2017
Keywords:
Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures
AIM: To investigate whether patients with refractory epilepsy and healthy infants differ in gut microbiota (GM), and how ketogenic diet (KD) alters GM. METHODS: A total of 14 epileptic and 30 healthy infants were recruited and seizure frequencies were recorded. Stool samples were collected for 16S rDNA sequencing using the Illumina Miseq platform. The composition of GM in each sample was analyzed with MOTHUR, and inter-group comparison was conducted by R software. RESULTS: After being on KD treatment for a week, 64% of epileptic infants showed an obvious improvement, with a 50% decrease in seizure frequency. GM structure in epileptic infants (P1 group) differed dramatically from that in healthy infants (Health group). Proteobacteria, which had accumulated significantly in the P1 group, decreased dramatically after KD treatment (P2 group). Cronobacter predominated in the P1 group and remained at a low level both in the Health and P2 groups. Bacteroides increased significantly in the P2 group, in which Prevotella and Bifidobacterium also grew in numbers and kept increasing. CONCLUSION: GM pattern in healthy infants differed dramatically from that of the epileptic group. KD could significantly modify symptoms of epilepsy and reshape the GM of epileptic infants.
Experiment 1
Needs review
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
- 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
- post-ketogenic diet (P2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pediatric patients with refractory epilepsy after ketogenic diet treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Supplementary Table 5
Description: Fecal microbiome of P2 group compared to healthy controls
Abundance in Group 1: increased abundance in post-ketogenic diet (P2)
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Needs review
Source: Supplementary Tables 4 & 5
Description: Fecal microbiome of P2 group compared to healthy controls
Abundance in Group 1: decreased abundance in post-ketogenic diet (P2)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Actinomycetota | ||
| Bifidobacterium | ||
| Bilophila | ||
| Clostridium | ||
| Escherichia | ||
| Faecalibacterium | ||
| Granulicatella | ||
| Haemophilus | ||
| Lachnoclostridium |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 2
Needs review
Differences from previous experiment shown
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 (P1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pediatric patients with refractory epilepsy before ketogenic diet treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Supplementary Table 5
Description: Fecal microbiome of P1 group compared to healthy controls
Abundance in Group 1: increased abundance in pre-ketogenic diet (P1)
Revision editor(s): Kavyaayala, WikiWorks
Signature 2
Needs review
Source: Supplementary Tables 4 & 5
Description: Fecal microbiome of P1 group compared to healthy controls
Abundance in Group 1: decreased abundance in pre-ketogenic diet (P1)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Atopobium | ||
| Bacteroides | ||
| Bacteroidota | ||
| Bifidobacterium | ||
| Bilophila | ||
| Clostridium | ||
| Escherichia | ||
| Granulicatella | ||
| Haemophilus |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 3
Needs review
Differences from previous experiment shown
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
- healthy controls and P1 group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-ketogenic diet (P2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pediatric patients with refractory epilepsy after ketogenic diet treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Needs review
Source: Figure 4
Description: Fecal microbiome of P2 group compared to healthy controls and P1 group
Abundance in Group 1: increased abundance in post-ketogenic diet (P2)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillaceae | ||
| Bacillales | ||
| Bacillus | ||
| Brochothrix | ||
| Eggerthella | ||
| Eggerthellaceae | ||
| Eggerthellales | ||
| Listeriaceae | ||
| Odoribacter | ||
| Parvimonas | ||
| Peptoclostridium | ||
| Solobacterium |
Revision editor(s): Kavyaayala, WikiWorks
Experiment 4
Needs review
Differences from previous experiment shown
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 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls and P2 group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-ketogenic diet (P1)
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 4
Description: Fecal microbiome of P1 group compared to healthy controls and P2 group
Abundance in Group 1: increased abundance in pre-ketogenic diet (P1)
Revision editor(s): Kavyaayala, WikiWorks
Experiment 5
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 and P2 groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- healthy infants
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 4
Description: Fecal microbiome of healthy controls compared to P1 and P2 groups
Abundance in Group 1: increased abundance in healthy controls
Revision editor(s): Kavyaayala, WikiWorks
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