Changes and significance of gut microbiota in children with focal epilepsy before and after treatment
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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
Zhou C, Gong S, Xiang S, Liang L, Hu X, Huang R, Liao Z, Ma Y, Xiao Z, Qiu J
Journal
Frontiers in cellular and infection microbiology
Year
2022
Keywords:
16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota
OBJECTIVE: To better understand the alterations in gut microbiota and metabolic pathways in children with focal epilepsy, and to further investigate the changes in the related gut microbiota and metabolic pathways in these children before and after treatment. METHODS: Ten patients with newly diagnosed focal epilepsy in Hunan Children's Hospital from April, 2020 to October, 2020 were recruited into the case group. The case group was further divided into a pre-treatment subgroup and a post-treatment subgroup. Additionally, 14 healthy children of the same age were recruited into a control group. The microbial communities were analyzed using 16s rDNA sequencing data. Metastas and LEfSe were used to identify different bacteria between and within groups. The Kyoto Encyclopedia of Genes and Genomes database was used to KEGG enrichment analysis. RESULTS: There were significant differences in α diversity among the pre-treatment, post-treatment, and control groups. Besides, the differences in gut microbiota composition in 3 groups were identified by principal co-ordinates analysis (PCoA), which showed a similar composition of the pre-treatment and post-treatment subgroups. At the phyla level, the relative abundance of Actinobacteria in the pre-treatment subgroup was significantly higher than that in the control group, which decreased significantly after 3 months of treatment and showed no significant difference between the control group. In terms of the genus level, Escherichia/Shigella, Streptococcus, Collinsella, and Megamonas were enriched in the pre-treatment subgroup, while Faecalibacterium and Anaerostipes were enriched in the control group. The relative abundance of Escherichia/Shigella, Streptococcus, Collinsella, and Megamonas was reduced significantly after a three-month treatment. Despite some genera remaining significantly different between the post-treatment subgroup and control group, the number of significantly different genera decreased from 9 to 4 through treatment. Notably, we found that the carbohydrate metabolism, especially succinate, was related to focal epilepsy. CONCLUSION: Children with focal epilepsy compared with healthy controls were associated with the statistically significant differences in the gut microbiota and carbohydrate metabolism. The differences were reduced and the carbohydrate metabolism improved after effective treatment. Our research may provide new directions for understanding the role of gut microbiota in the pathogenesis of focal epilepsy and better alternative treatments.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
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 control (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-treatment (focal epilepsy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These are individuals with newly diagnosed focal epilepsy before they started receiving treatment.
- 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
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 3
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: Figure 2D
Description: Diversity and relative abundance of gut microbiota between the group before treatment and the control group
Abundance in Group 1: increased abundance in pre-treatment (focal epilepsy)
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-treatment (focal epilepsy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: Fig.4D
Description: Diversity and relative abundance of gut microbiota between the group after treatment and the control group
Abundance in Group 1: increased abundance in post-treatment (focal epilepsy)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricimonas | ||
| Collinsella | ||
| Coriobacteriales | ||
| Eubacteriaceae | ||
| Eubacterium | ||
| Oscillibacter | ||
| Parabacteroides | ||
| Parabacteroides merdae | ||
| Alistipes indistinctus | ||
| uncultured organism |
Revision editor(s): Chinelsy
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to oxcarbazepine Response to oxcarbazepine,response to oxcarbazepine
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-treatment (focal epilepsy)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: Fig.3D
Description: Diversity and relative abundance of gut microbiota between the groups before and after treatment
Abundance in Group 1: increased abundance in post-treatment (focal epilepsy)
| NCBI | Quality Control | Links |
|---|---|---|
| Lentisphaeria | ||
| Oscillibacter | ||
| Sutterellaceae | ||
| Victivallaceae | ||
| Victivallales | ||
| Victivallis | ||
| Oscillibacter sp. G2 | ||
| Victivallaceae bacterium NML 080035 | ||
| uncultured rumen bacterium |
Revision editor(s): Chinelsy
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: Fig.3D
Description: Diversity and relative abundance of gut microbiota between the groups before and after treatment
Abundance in Group 1: decreased abundance in post-treatment (focal epilepsy)
Revision editor(s): Chinelsy
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
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 control (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-treatment (focal epilepsy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These are individuals with newly diagnosed focal epilepsy before they started receiving treatment.
Lab analysis
Statistical Analysis
- Statistical test
- Metastats
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: Supplementary Figure 1
Description: Significant results of Metastats analysis at the phyla and genus level
Abundance in Group 1: increased abundance in pre-treatment (focal epilepsy)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Faecalibacterium | ||
| Parabacteroides | ||
| Escherichia/Shigella sp. | ||
| Megamonas | ||
| Streptococcus | ||
| Romboutsia | ||
| Collinsella |
Revision editor(s): Folakunmi
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-treatment (focal epilepsy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: Supplementary Figure 3
Description: Significant results of Metastats analysis at the phyla and genus level
Abundance in Group 1: increased abundance in post-treatment (focal epilepsy)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Parabacteroides | ||
| Anaerostipes | ||
| Oscillibacter | ||
| Megamonas |
Revision editor(s): Folakunmi
Experiment 6
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to oxcarbazepine Response to oxcarbazepine,response to oxcarbazepine
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-treatment (focal epilepsy)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
Source: supplementary figure 3
Description: Significant results of Metastats analysis at the phyla and genus levels
Abundance in Group 1: increased abundance in post-treatment (focal epilepsy)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Blautia | ||
| Escherichia/Shigella sp. | ||
| Megamonas | ||
| Oscillibacter | ||
| Streptococcus | ||
| Romboutsia | ||
| Collinsella | ||
| Anaerostipes |
Revision editor(s): Folakunmi
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