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
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 PD according to the UK Brain Bank criteria by a movement disorder specialist, and the original Hoehn + Yahr scale was followed for disease staging
- 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
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.025
- 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
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 | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Lentisphaeria | ||
| Verrucomicrobiales | ||
| Verrucomicrobiia | ||
| Verrucomicrobiota | ||
| Victivallales | ||
| Lactobacillaceae |
Revision editor(s): Karima
Signature 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
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.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- The use of probiotics and antibiotics was an exclusion criterion for patients and their healthy spouses.
Lab analysis
Statistical Analysis
- 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
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
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
Differences from previous experiment shown
Subjects
- 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
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
- Sequencing type
- Not specified
- 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
- Not specified
- Statistical test
- Not specified
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
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