Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease
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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
Nishiwaki H, Ueyama J, Ito M, Hamaguchi T, Takimoto K, Maeda T, Kashihara K, Tsuboi Y, Mori H, Kurokawa K, Katsuno M, Hirayama M, Ohno K
Journal
NPJ Parkinson's disease
Year
2024
We aimed to identify gut microbial features in Parkinson's disease (PD) across countries by meta-analyzing our fecal shotgun sequencing dataset of 94 PD patients and 73 controls in Japan with five previously reported datasets from USA, Germany, China1, China2, and Taiwan. GC-MS and LC-MS/MS assays were established to quantify fecal short-chain fatty acids (SCFAs) and fecal polyamines, respectively. α-Diversity was increased in PD across six datasets. Taxonomic analysis showed that species Akkermansia muciniphila was increased in PD, while species Roseburia intestinalis and Faecalibacterium prausnitzii were decreased in PD. Pathway analysis showed that genes in the biosyntheses of riboflavin and biotin were markedly decreased in PD after adjusting for confounding factors. Five out of six categories in carbohydrate-active enzymes (CAZymes) were decreased in PD. Metabolomic analysis of our fecal samples revealed that fecal SCFAs and polyamines were significantly decreased in PD. Genes in the riboflavin and biotin biosyntheses were positively correlated with the fecal concentrations of SCFAs and polyamines. Bacteria that accounted for the decreased riboflavin biosynthesis in Japan, the USA, and Germany were different from those in China1, China2, and Taiwan. Similarly, different bacteria accounted for decreased biotin biosynthesis in the two country groups. We postulate that decreased SCFAs and polyamines reduce the intestinal mucus layer, which subsequently facilitates the formation of abnormal α-synuclein fibrils in the intestinal neural plexus in PD, and also cause neuroinflammation in PD.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Subjects
- Location of subjects
- China
- Germany
- Japan
- United States of America
- Taiwan
- 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
- 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 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
- Parkinson’s disease patients (PD patients)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refers to patients with idiopathic PD and was diagnosed according to the Movement Disorder Society’s (MDS) PD criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 73
- Group 1 sample size Number of subjects in the case (exposed) group
- 94
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Source: Supplementary Table 7
Description: Meta-analysis of species and genera in six datasets
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Source: Supplementary Table 7
Description: Meta-analysis of species and genera in six datasets
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- arcsine square-root
- Statistical test
- MaAsLin2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Source: Supplementary Table 8
Description: Confounding factor analysis of the species and the genera that were significantly changed in meta-analysis of six datasets
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Source: Supplementary Table 8
Description: Confounding factor analysis of the species and the genera that were significantly changed in meta-analysis of six datasets
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
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