Altered composition of the gut microbiome in patients with drug-resistant epilepsy

From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 16 December 2021
study design
cross-sectional observational, not case-control
Citation
PMID
URI
Authors
Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J, Chen L
Journal
Epilepsy research
Year
2018
OBJECTIVE: The relationship between the gut microbiota and the central nervous system has been gradually recognized while whether microbiome plays a role in the pathogenesis of drug-resistant epilepsy is still unknown. The aim of our work was to explore whether dysbiosis is involved in the mechanism of drug-resistant epilepsy. METHODS: Patients with epilepsy attending West China Hospital of Sichuan University were enrolled from March to May 2017. Patients were grouped into drug-resistant (n = 42) and drug-sensitive (n = 49) groups, another 65 healthy controls were from the same families of the patients. The fecal samples were collected and the microbiome composition was analyzed by high-throughout sequencing of the 16s ribosomal DNA. RESULTS: We found that the gut microbial community of drug-resistant epilepsy was significantly altered with an abnormal increased abundance of rare flora. While the gut microbiome composition of drug-sensitive epilepsy was similar with that of healthy controls. Specifically, patients with four seizures per year or fewer showed an increase of Bifidobacteria and Lactobacillus than those with more than four seizures per year. CONCLUSIONS: Dysbiosis may be involved in the mechanism of drug-resistant epilepsy and restoring the gut microbial community may be a novel therapeutic method for drug-resistant epilepsy.

Experiment 1


Reviewed Marked as Reviewed by Lwaldron on 16 December 2021

Curated date: 2021/12/16

Curator: Fatima

Revision editor(s): WikiWorks753, Fatima

Subjects

Location of subjects Country from which study subjects were recruited
China
Host species Species from which microbiome was sampled (if applicable)
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
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)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Drug sensitive epilepsy
Group 1 name Corresponds to the case (exposed) group for case-control studies
Drug resistant epilepsy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE)
Group 0 sample size Number of subjects in the control (unexposed) group
49
Group 1 sample size Number of subjects in the case (exposed) group
42
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 Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
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
2


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
increased

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 16 December 2021

Curated date: 2021/12/16

Curator: Fatima

Revision editor(s): Fatima

Source: Figure 2

Description: Lefse analysis showing microbiome differences in patients with drug sensitive epilepsy and drug sensitive epilepsy

Abundance in Group 1: decreased abundance in Drug resistant epilepsy

NCBI Links
Bacteria
Bacteroidaceae
Bacteroidales
Bacteroides
Bacteroidota
Bacteroidia
Barnesiella

Revision editor(s): Fatima

Signature 2

Reviewed Marked as Reviewed by Fatima on 16 February 2022

Curated date: 2021/12/16

Curator: Fatima

Revision editor(s): Fatima

Source: Figure 2

Description: Lefse analysis showing microbiome differences among drug resistance and drug sensitive epilepsy

Abundance in Group 1: increased abundance in Drug resistant epilepsy

NCBI Links
Erysipelotrichia
Moraxellaceae
Firmicutes
Lachnospiraceae
Negativicutes
Selenomonadales
Roseburia
Phascolarctobacterium
Acidaminococcaceae
Methanobacteria
Methanobacteriaceae
Methanobrevibacter
Methanobacteriales
Fusobacteria
Fusobacteriia
Fusobacteriaceae
Fusobacteriales
Fusobacterium
Coprococcus
Neisseriales
Neisseria
Neisseriaceae
Archaea
Euryarchaeota
Verrucomicrobiales
Verrucomicrobia
Akkermansia
Verrucomicrobiaceae
Verrucomicrobiae
Gemmiger
Ruminococcus
Paraprevotella
Coprobacillus
Delftia
Candidatus Saccharibacteria
Dorea
Holdemania
Erysipelotrichaceae
Atopobium
Erysipelotrichales

Revision editor(s): Fatima

Experiment 2


Reviewed Marked as Reviewed by Lwaldron on 16 December 2021

Curated date: 2021/12/16

Curator: Fatima

Revision editor(s): WikiWorks753, Fatima

Subjects

Location of subjects Country from which study subjects were recruited
China
Host species Species from which microbiome was sampled (if applicable)
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
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)
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
Drug resistant epilepsy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Drug sensitive epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE)
Group 0 sample size Number of subjects in the control (unexposed) group
65
Group 1 sample size Number of subjects in the case (exposed) group
49
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 Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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
2


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