Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Italy
- 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
- Parkinson's disease patients with Tremor Dominant - TD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease patients with Akinetic Rigid - AR
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A phenotype category based on motor signs
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months prior to enrollment
Lab analysis
- Sequencing type
- 16S
- 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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, smoking status, Confounders controlled for: "coffee consumption" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.coffee consumption, Confounders controlled for: "pharmacological treatment" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.pharmacological treatment
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3a
Description: Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (a) Positive LDA score (green) highlights the enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows the enriched taxa in PD patients with Akinetic Rigid (AR);
Abundance in Group 1: increased abundance in Parkinson's disease patients with Akinetic Rigid - AR
| NCBI | Quality Control | Links |
|---|---|---|
| Sedimentibacter | ||
| Serratia | ||
| Escherichia | ||
| Enterobacteriaceae |
Revision editor(s): Junie, Peace Sandy
Signature 2
Source: Figure 3a
Description: Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (a) Positive LDA score (green) highlights the enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows the enriched taxa in PD patients with Akinetic Rigid (AR);
Abundance in Group 1: decreased abundance in Parkinson's disease patients with Akinetic Rigid - AR
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lachnospiraceae | ||
| Clostridiaceae | ||
| Faecalibacterium | ||
| Blautia | ||
| Coprococcus | ||
| Lachnospira | ||
| Tindallia | ||
| Gemellaceae | ||
| Gemella | ||
| Brevibacteriaceae | ||
| Brevibacterium |
Revision editor(s): Junie, Peace Sandy
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Parkinson's disease patients with Tremor Dominant - TD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease patients with Diskinetic - D
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3B
Description: Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size(Linear discriminant analysis (LDA) score (log 10) > 2). (b) Positive LDA score (green) highlights enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows enriched taxa in PD with Dyskinetic (D)
Abundance in Group 1: increased abundance in Parkinson's disease patients with Diskinetic - D
| NCBI | Quality Control | Links |
|---|---|---|
| Serratia | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Escherichia | ||
| Enterobacteriaceae |
Revision editor(s): Peace Sandy
Signature 2
Source: Figure 3B
Description: Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size(Linear discriminant analysis (LDA) score (log 10) > 2). (b) Positive LDA score (green) highlights enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows enriched taxa in PD with Dyskinetic (D)
Abundance in Group 1: decreased abundance in Parkinson's disease patients with Diskinetic - D
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Parkinson's disease patients with Diskinetic - D
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease patients with Akinetic Rigid - AR
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body mass index, Confounders controlled for: "coffe consumption" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.coffe consumption, smoking status, Confounders controlled for: "pharmalogical treatment" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.pharmalogical treatment
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3C
Description: Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (c) Positive LDA score (green) highlights enriched taxa in PD patients with Dyskinetic
Abundance in Group 1: decreased abundance in Parkinson's disease patients with Akinetic Rigid - AR
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillaceae |
Revision editor(s): Peace Sandy
