Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study
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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
Babacan Yildiz G, Kayacan ZC, Karacan I, Sumbul B, Elibol B, Gelisin O, Akgul O
Journal
Acta neurologica Belgica
Year
2023
Keywords:
16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease
OBJECTIVE: The investigations related to how gut microbiota changes the brain-gut axis in idiopathic Parkinson's disease (PD) attract growing interest. We aimed to determine whether gut microbiota is altered in PD patients and whether non-motor symptoms of PD and disease duration had any relation with alterations of microbiota profiles among patients. METHODS: Microbial taxa in stool samples obtained from 84 subjects (42-PD patients and 42-healthy spouses) were analyzed using 16S rRNA amplicon-sequencing. RESULTS: We observed a significant decrease of Firmicutes and a significant increase of Verrucomicrobiota at the phylum level. At the family level, Lactobacillaceae and Akkermansiaceae were significantly increased and Coriobacteriales Incertae Sedis were significantly decreased in the PD patients compared to their healthy spouses. Genus level comparison inferred significant increase in abundance only in Lactobacillus while the abundance of Lachnospiraceae ND3007 group, Tyzzerella, Fusicatenibacter, Eubacterium hallii group and Ruminococcus gauvreauii group were all decreased. We determined that the abundance of Prevotella genus decreased, but not significantly in PD patients. In addition, we found differences in microbiota composition between patients with and without non-motor symptoms. CONCLUSION: We observed differences in gut microbiota composition between PD patients and their healthy spouses. Our findings suggest that disease duration influenced microbiota composition, which in turn influenced development of non-motor symptoms in PD. This study is the first in terms of both gut microbiota research in Turkish PD patients and the probable effect of microbiota on non-motor symptoms of PD.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Subjects
- Location of subjects
- Turkey
- 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 spouses
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients were diagnosed with idiopathic Parkinson's disease (PD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- 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
- 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).
- arcsine square-root
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 2
Description: Significantly Increased different taxa in relative abundances between PD patients and healthy control
Abundance in Group 1: increased abundance in Patients with Parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcales | ||
| Akkermansiaceae | ||
| Bacilli | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Lentisphaeria | ||
| Verrucomicrobiales | ||
| Verrucomicrobiia | ||
| Verrucomicrobiota | ||
| Victivallales |
Revision editor(s): Karima
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 2
Description: Significantly decreased different taxa in relative abundances between PD patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with Parkinson's disease
Revision editor(s): Karima
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- more than 5 years PD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients were diagnosed with idiopathic PD according to the UK Brain Bank criteria by a movement disorder specialist, and the original Hoehn + Yahr scale was followed for disease staging
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 3
Description: Comparison of Taxa Relative Abundances Among PD Patients Based on Disease Duration (≥5 Years)
Abundance in Group 1: decreased abundance in more than 5 years PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Cyanobacteriota |
Revision editor(s): Karima
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients with REM sleep behavior disorder
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who has Parkinson's disease and REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Fig. 2
Description: Genus found to be significantly increased in PD patients with RBD
Abundance in Group 1: increased abundance in PD patients with REM sleep behavior disorder
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Karima
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Fig. 2
Description: Genus found to be significantly changed in PD patients with RBD
Abundance in Group 1: decreased abundance in PD patients with REM sleep behavior disorder
| NCBI | Quality Control | Links |
|---|---|---|
| Fusicatenibacter | ||
| Lachnospiraceae ND3007 groupLachnospiraceae ND3007 group |
Revision editor(s): Karima
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients without RBD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who has Parkinson's disease without REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Fig. 2
Description: Genus found to be significantly changed in PD patient without RBD
Abundance in Group 1: decreased abundance in PD patients without RBD
| NCBI | Quality Control | Links |
|---|---|---|
| Fusicatenibacter | ||
| Lactobacillus | ||
| Lachnospiraceae ND3007 groupLachnospiraceae ND3007 group |
Revision editor(s): Karima, KateRasheed
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD patients without constipation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients with constipation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients who has constipation
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 3
Description: Comparison of taxa relative abundances among PD patients with and without constipation
Abundance in Group 1: increased abundance in PD patients with constipation
| NCBI | Quality Control | Links |
|---|---|---|
| Mediterraneibacter gnavus |
Revision editor(s): Karima
Experiment 7
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD patients without RBD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients with RBD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who has Parkinson's disease and REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 3
Description: Comparison of taxa relative abundances among PD patients with and without RBD
Abundance in Group 1: decreased abundance in PD patients with RBD
Revision editor(s): Karima
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 3
Description: Comparison of taxa relative abundances among PD patients with and without RBD
Abundance in Group 1: increased abundance in PD patients with RBD
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Acidaminococcus |
Revision editor(s): Karima
Experiment 8
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD patients without anosmia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients with anosmia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's Disease patient who has lost of the ability to detect one or more smells
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-2
Source: Table 3
Description: Comparison of taxa relative abundances among PD patients with and without anosmia
Abundance in Group 1: increased abundance in PD patients with anosmia
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobiaceae | ||
| Bacilli | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Karima
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