Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis
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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 Uniform resource identifier for web resources.
Authors
Kleine Bardenhorst S, Cereda E, Severgnini M, Barichella M, Pezzoli G, Keshavarzian A, Desideri A, Pietrucci D, Aho VTE, Scheperjans F, Hildebrand F, Weis S, Egert M, Karch A, Vital M, Rübsamen N
Journal
European journal of neurology
Year
2023
Keywords:
Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review
BACKGROUND AND PURPOSE: The role of the gut microbiome in the pathogenesis of Parkinson disease (PD) is under intense investigation, and the results presented are still very heterogeneous. These discrepancies arise not only from the highly heterogeneous pathology of PD, but also from widely varying methodologies at all stages of the workflow, from sampling to final statistical analysis. The aim of the present work is to harmonize the workflow across studies to reduce the methodological heterogeneity and to perform a pooled analysis to account for other sources of heterogeneity. METHODS: We performed a systematic review to identify studies comparing the gut microbiota of PD patients to healthy controls. A workflow was designed to harmonize processing across all studies from bioinformatics processing to final statistical analysis using a Bayesian random-effects meta-analysis based on individual patient-level data. RESULTS: The results show that harmonizing workflows minimizes differences between statistical methods and reveals only a small set of taxa being associated with the pathogenesis of PD. Increased shares of the genera Akkermansia and Bifidobacterium and decreased shares of the genera Roseburia and Faecalibacterium were most characteristic for PD-associated microbiota. CONCLUSIONS: Our study summarizes evidence that reduced levels of butyrate-producing taxa in combination with possible degradation of the mucus layer by Akkermansia may promote intestinal inflammation and reduced permeability of the gut mucosal layer. This may allow potentially pathogenic metabolites to transit and enter the enteric nervous system.
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-9
Subjects
- Location of subjects
- China
- Finland
- Germany
- Italy
- United States of America
- 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 Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's Disease (PD) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 751
- Group 1 sample size Number of subjects in the case (exposed) group
- 1092
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- log transformation
- Statistical test
- ANCOM-BC
- 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
- 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 KateRasheed on 2025-7-9
Source: Figure 4
Description: Differentially abundant bacterial taxa in Parkinson's Disease patients
Abundance in Group 1: increased abundance in Parkinson's Disease (PD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacteriaceae | ||
| Bifidobacterium |
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-9
Source: Figure 4
Description: Differentially abundant bacterial taxa in Parkinson's Disease patients
Abundance in Group 1: decreased abundance in Parkinson's Disease (PD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Faecalibacterium | ||
| Roseburia | ||
| Butyricicoccus | ||
| Fusicatenibacter | ||
| Lachnospiraceae |
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-9
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 KateRasheed on 2025-7-9
Source: Table 2
Description: Significant bacterial taxa identified while comparing individuals with Parkinson’s Disease (PD) to healthy controls (Results from a pooled analysis).
Abundance in Group 1: increased abundance in Parkinson's Disease (PD) patients
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-9
Source: Table 2
Description: Significant bacterial taxa identified while comparing individuals with Parkinson’s Disease (PD) to healthy controls (Results from a pooled analysis).
Abundance in Group 1: decreased abundance in Parkinson's Disease (PD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnospiraceae | ||
| Roseburia |
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-7-9
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).
- centered log-ratio
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 KateRasheed on 2025-7-9
Source: Table SE1
Description: Differentially abundant bacterial taxa identified in a sub group meta analysis with confounders controlled for age and sex
Abundance in Group 1: increased abundance in Parkinson's Disease (PD) patients
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-9
Source: Table SE1
Description: Differentially abundant bacterial taxa identified in a sub group meta analysis with confounders controlled for age and sex
Abundance in Group 1: decreased abundance in Parkinson's Disease (PD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Butyricicoccus | ||
| Enterobacteriaceae | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Lachnospiraceae | ||
| Prevotella | ||
| Pseudomonadota | ||
| Roseburia |
Revision editor(s): Ese
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