A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study
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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
Lee H, Lee S, Lee DH, Kim DW
Journal
Epilepsy research
Year
2021
Keywords:
Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus
BACKGROUND: Approximately one-third of epilepsy patients suffer from drug-resistant epilepsy. The gut microbiome, which is the total genetic makeup of all of the total microbes inhabiting the gut, can affect the CNS through various mechanisms. However, there are only limited studies about the relationship between the gut microbiome and epilepsy. We investigated the composition and characteristics of the gut microbiota among adult patients who have drug-responsive and drug-resistant epilepsy. METHODS: We prospectively included 44 adult epilepsy patients and classified them into drug-responsive and drug-resistant groups. We collected fecal samples for the next-generation sequencing analysis. We statistically estimated the bacterial differences and alpha and beta diversities in each category. RESULTS: Although there was no difference in demographic factors between the drug-responsive and drug-resistant groups, there was a significant difference in the composition of the gut microbiota. While the relative abundance of Bacteroides finegoldii and Ruminococcus_g2 increased in the drug-responsive group, the relative abundance of Negativicutes, which belong to Firmicutes increased in the drug-resistant group. Bifidobacterium was relatively abundant in epilepsy patients with a normal electroencephalogram. There was no significant difference between the two groups in analyses of alpha and beta diversities. CONCLUSIONS: We found a significant difference in the composition of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy. Difference in gut microbiota can be used as a novel biomarker to predict prognosis and evaluate treatment response in epilepsy patients. In addition, modification of gut microbiome can be an effective treatment strategy for patient with drug-resistant epilepsy.
Experiment 1
Needs review
Subjects
- Location of subjects
- South Korea
- 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
- drug-resistant
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- drug-responsive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- drug-responsive epilepsy group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- 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
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Figure 3a/3b
Description: Comparing fecal microbiome of drug-responsive epilepsy group to drug-resistant epilepsy group
Abundance in Group 1: increased abundance in drug-responsive
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides finegoldii | ||
| Mediterraneibacter faecis | ||
| Ruminococcus | ||
| HQ785065_sHQ785065_s | ||
| AM275462_sAM275462_s |
Revision editor(s): Kavyaayala
Signature 2
Needs review
Source: Figure 3a/3b
Description: Comparing fecal microbiome of drug-responsive epilepsy group to drug-resistant epilepsy group
Abundance in Group 1: decreased abundance in drug-responsive
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Megamonas funiformis | ||
| Negativicutes | ||
| Selenomonadaceae | ||
| Selenomonadales | ||
| Veillonellaceae | ||
| Veillonellales |
Revision editor(s): Kavyaayala
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal brain MRI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- abnormal brain MRI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- abnormal results from magnetic resonance imaging
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
incomplete
Source: Figure 4a/4b
Description: Comparing fecal microbiome of those with abnormal brain MRI to those with normal brain MRI
Abundance in Group 1: increased abundance in abnormal brain MRI
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Bacteroides finegoldii |
Revision editor(s): Kavyaayala
Signature 2
incomplete
Source: Figure 4a/4b
Description: Comparing fecal microbiome of those with abnormal brain MRI to those with normal brain MRI
Abundance in Group 1: decreased abundance in abnormal brain MRI
| NCBI | Quality Control | Links |
|---|---|---|
| DQ824928_gDQ824928_g | ||
| DQ824928_sDQ824928_s | ||
| Dialister | ||
| Veillonellales | ||
| Veillonellaceae | ||
| Shigella flexneri | ||
| Escherichia |
Revision editor(s): Kavyaayala
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal EEG
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- abnormal EEG
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- abnormal results from electroencephalogram
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
incomplete
Source: Figure 5a/5b
Description: Comparing fecal microbiome of those with abnormal EEG to those with normal EEG
Abundance in Group 1: increased abundance in abnormal EEG
Revision editor(s): Kavyaayala
Signature 2
incomplete
Source: Figure 5a/5b
Description: Comparing fecal microbiome of those with abnormal EEG to those with normal EEG
Abundance in Group 1: decreased abundance in abnormal EEG
Revision editor(s): Kavyaayala
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