Gut microbiome is not associated with mild cognitive impairment 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.
Authors
Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P, Wilmes P
Journal
NPJ Parkinson's disease
Year
2024
Gut microbiome differences between people with Parkinson's disease (PD) and control subjects without Parkinsonism are widely reported, but potential alterations related to PD with mild cognitive impairment (MCI) have yet to be comprehensively explored. We compared gut microbial features of PD with MCI (n = 58) to cognitively unimpaired PD (n = 60) and control subjects (n = 90) with normal cognition. Our results did not support a specific microbiome signature related to MCI in PD.
Experiment 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Subjects
- Location of subjects
- Luxembourg
- 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
- Control Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cognitively Unimpaired PD (PD-NC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients without cognitive impairment (NC).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 90
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
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).
- raw counts
- Statistical test
- DESeq2
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: increased abundance in Cognitively Unimpaired PD (PD-NC)
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Cognitively Unimpaired PD (PD-NC)
Revision editor(s): Aleru Divine
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cognitive impairment Abnormality of cognition,Cognitive abnormality,Cognitive defects,Cognitive deficits,Cognitive impairment,Intellectual impairment,cognitive impairment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cognitively Unimpaired-PD (PD-NC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Cognitive Impairment-PD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 60
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d and table 3c
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: increased abundance in Mild Cognitive Impairment-PD
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillales | ||
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Supplementary Figure 1d and table 3c
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Mild Cognitive Impairment-PD
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Asteroleplasma |
Revision editor(s): Aleru Divine
Experiment 3
Needs review
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 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Cognitive Impairment -PD (PD-MCI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients with Mild Cognitive Impairment (MCI).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 90
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: increased abundance in Mild Cognitive Impairment -PD (PD-MCI)
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Mild Cognitive Impairment -PD (PD-MCI)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccaceae | ||
| Clostridiaceae | ||
| Clostridium | ||
| Eubacteriales | ||
| Lachnospiraceae | ||
| Lachnospiraceae bacterium 10-1 | ||
| Prevotella | ||
| Romboutsia | ||
| Ruminococcaceae bacterium UCG-005 |
Revision editor(s): Aleru Divine
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cognitively Unimpaired PD (PD-NC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients without cognitive impairment (NC).
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: increased abundance in Cognitively Unimpaired PD (PD-NC)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiales bacterium DTU089 |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Cognitively Unimpaired PD (PD-NC)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Lachnospiraceae | ||
| Ruminococcaceae bacterium UCG-005 | ||
| Lachnospiraceae bacterium 10-1 |
Revision editor(s): Aleru Divine
Experiment 5
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Cognitive Impairment PD (PD-MCI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients with Mild Cognitive Impairment (NC).
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Mild Cognitive Impairment PD (PD-MCI)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccaceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Experiment 6
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cognitively Unimpaired PD (PD-NC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients without cognitive impairment (NC).
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
Lab analysis
Statistical Analysis
- Statistical test
- Linear Regression
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: increased abundance in Cognitively Unimpaired PD (PD-NC)
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Cognitively Unimpaired PD (PD-NC)
Revision editor(s): Aleru Divine
Experiment 7
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Cognitive Impairment PD (PD-MCI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients with Mild Cognitive Impairment (NC).
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Mild Cognitive Impairment PD (PD-MCI)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccaceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
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