Study information
incomplete
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Nishiwaki H, Ueyama J, Kashihara K, Ito M, Hamaguchi T, Maeda T, Tsuboi Y, Katsuno M, Hirayama M, Ohno K
Journal
NPJ Parkinson's disease
Year
2022
Gut microbiota and fecal bile acids were analyzed in 278 patients with α-synucleinopathies, which were comprised of 28 patients with dementia with Lewy bodies (DLB), 224 patients with Parkinson's disease (PD), and 26 patients with idiopathic rapid eye movement sleep behavior disorder (iRBD). Similarly to PD, short-chain fatty acids-producing genera were decreased in DLB. Additionally, Ruminococcus torques and Collinsella were increased in DLB, which were not changed in PD. Random forest models to differentiate DLB and PD showed that high Ruminococcus torques and high Collinsella, which presumably increase intestinal permeability, as well as low Bifidobacterium, which are also observed in Alzheimer's disease, were predictive of DLB. As Ruminococcus torques and Collinsella are also major secondary bile acids-producing bacteria, we quantified fecal bile acids and found that the production of ursodeoxycholic acid (UDCA) was high in DLB. Increased UDCA in DLB may mitigate neuroinflammation at the substantia nigra, whereas neuroinflammation may not be critical at the neocortex. Theraeutic intervention to increase Bifidobacteirum and its metabolites may retard the development and progression of DLB.
Experiment 1
incomplete
Subjects
- Location of subjects
- Japan
- 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
- Lewy body dementia dementia with Lewy bodies,dementia, Lewy body,diffuse Lewy body disease,diffuse Lewy body disease with gaze palsy,DLB,Lewy body dementia,Lewy body disease,Lewy body variant of Alzheimer disease,Senile dementia of the Lewy body type,lewy body dementia
- 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
- DLB patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Dementia with Lewy bodies (DLB)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 147
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Yes, excluded those DLB patients who took antibiotics in the past 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
- ANCOM-BC
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, constipation, proton-pump inhibitor
Signature 1
incomplete
Source: Supplementary Table 2a
Description: Taxa enriched in DLB patients.
Abundance in Group 1: increased abundance in DLB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella | ||
| Eggerthella | ||
| [Ruminococcus] torques |
Revision editor(s): Kristin.abraham
Signature 2
incomplete
Source: Supplementary Table 2a
Description: Taxa depleted in DLB patients.
Abundance in Group 1: decreased abundance in DLB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Lachnospiraceae | ||
| Butyricicoccus | ||
| Coprococcus | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Haemophilus |
Revision editor(s): Kristin.abraham
Signature 3
incomplete
Source:
Description:
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Kristin.abraham
Experiment 2
incomplete
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parkinson's disease IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Parkinson's Disease (PD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 224
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
Signature 1
incomplete
Source: Supplementary Table 3a
Description: Taxa enriched in PD patients.
Abundance in Group 1: increased abundance in PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter | ||
| Akkermansia |
Revision editor(s): Kristin.abraham
Signature 2
incomplete
Source: Supplementary Table 3a
Description: Taxa depleted in PD patients.
Abundance in Group 1: decreased abundance in PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Coprococcus | ||
| Blautia | ||
| Monoglobus | ||
| Fusicatenibacter | ||
| Lachnospiraceae | ||
| Agathobacter |
Revision editor(s): Kristin.abraham
Experiment 3
incomplete
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lewy body dementia , Parkinson's disease dementia with Lewy bodies,dementia, Lewy body,diffuse Lewy body disease,diffuse Lewy body disease with gaze palsy,DLB,Lewy body dementia,Lewy body disease,Lewy body variant of Alzheimer disease,Senile dementia of the Lewy body type,lewy body dementia,IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HY3&4 PD patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- DLB patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Dementia with Lewy bodies (DLB)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 91
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Yes, excluded patients with recent antibiotic use within the past 1 month.
Lab analysis
Statistical Analysis
- Statistical test
- Random Forest Analysis
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
incomplete
Source: Supplementary Table 6; Supplementary Table 7a
Description: Taxa enriched in DLB patients
Abundance in Group 1: increased abundance in DLB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella | ||
| [Ruminococcus] torques |
Revision editor(s): Kristin.abraham
Signature 2
incomplete
Source: Supplementary Table 6; Supplementary Table 7a
Description: Taxa depleted in DLB patients
Abundance in Group 1: decreased abundance in DLB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Kristin.abraham
Experiment 4
incomplete
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PDD+ patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
Lab analysis
Statistical Analysis
- Statistical test
- ANCOM-BC
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body mass index, constipation, proton-pump inhibitor
Signature 1
incomplete
Source: Supplementary Table 7b
Description: Taxa enriched in DLB patients
Abundance in Group 1: increased abundance in DLB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella |
Revision editor(s): Kristin.abraham
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