The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies
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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
- Australia
- 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
- Household Control (HC) at t=0 to t=12
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease (PD) patients at t=0 to t=12
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson disease patients on existing therapy regimes at t=0 to t=12
- Group 0 sample size Number of subjects in the control (unexposed) group
- 74
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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).
- centered log-ratio
- Statistical test
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- 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
- region of residence
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the family levels (represented by red dots) were apparent and indicative of a PD-related GM composition.
Abundance in Group 1: increased abundance in Parkinson's disease (PD) patients at t=0 to t=12
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Signature 2
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the family levels (represented by red dots) were apparent and indicative of a PD-related GM composition.
Abundance in Group 1: decreased abundance in Parkinson's disease (PD) patients at t=0 to t=12
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccaceae |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with Slow progressing Parkinson's disease at t=0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Faster progressing Parkinson's disease at t=0
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with faster progressing parkinson's disease over a 12 month period at t=0
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Differential abundance of taxa between faster progressing and slower progressing PD patients within 12 months at t=0 (family taxonomic level)
Abundance in Group 1: decreased abundance in Patients with Faster progressing Parkinson's disease at t=0
| NCBI | Quality Control | Links |
|---|---|---|
| Barnesiellaceae |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Experiment 3
Curated date: 2024/03/13
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with Slow progressing Parkinson's disease at t=0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Faster progressing Parkinson's disease at t=0
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with faster progressing parkinson's disease over a 12 month period at t=0
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Differential abundance of taxa between faster progressing and slower progressing PD patients within 12 months at t=0 to t=12 (genus taxonomic level)
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Barnesiella |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 6)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Deep Brain Stimulation DAT patients (t = 0 to t = 6)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Deep Brain Stimulation DAT patients after initiation of DBS therapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
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
Signature 1
Source: Figure 7
Description: Results across genus taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 6)
Abundance in Group 1: increased abundance in Deep Brain Stimulation DAT patients (t = 0 to t = 6)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 5
Curated date: 2024/03/16
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Deep Brain Stimulation DAT patients
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
Signature 3
Source: Figure 7
Description: Results across family taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 12).
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobacteriaceae | ||
| Bacillaceae | ||
| Spirochaetaceae |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 6
Curated date: 2024/03/16
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 12).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Deep Brain Stimulation DAT patients (t = 0 to t = 12).
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
Signature 1
Source: Figure 7
Description: Results across genus taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 12).
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Methanobrevibacter | ||
| Treponema | ||
| Bacillus | ||
| Veillonella | ||
| Citrobacter | ||
| Faecalicoccus | ||
| Morganella |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Signature 3
Source: Figure 7
Description: Results across genus taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 12).
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Hespellia | ||
| Acetanaerobacterium | ||
| Anaerotruncus | ||
| Howardella | ||
| Flavonifractor |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Experiment 7
Curated date: 2024/03/16
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 6)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Deep Brain Stimulation DAT patients (t = 0 to t = 6)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Deep Brain Stimulation DAT patients in response to LCIG therapy initiation and continuation (t=0 to t=6)
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
Signature 1
Source: figure 7
Description: The most differentially abundant taxa after the initiation of LCIG therapy at the genus level over the (t = 0 to t = 6) interval.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Experiment 9
Curated date: 2024/03/16
Curator:
Revision editor(s):
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
Signature 1
Source: Figure 7
Description: The most differentially abundant taxa after the initiation of LCIG therapy at the family level over the (t = 0 to t = 6) interval.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Signature 2
Source: Figure 7
Description: The most differentially abundant taxa after the initiation of LCIG therapy at the family level over the (t = 0 to t = 6) interval.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Acetanaerobacterium | ||
| Eggerthella | ||
| Gordonibacter | ||
| Hespellia | ||
| Holdemania |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 12)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Deep Brain Stimulation DAT patients (t = 0 to t = 12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Deep Brain Stimulation DAT patients in response to LCIG therapy initiation and continuation (t=0 to t=12)
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
Signature 1
Source: Figure 7
Description: The most differentially abundant taxa after the initiation of LCIG therapy at the family level over the (t = 0 to t = 12) interval.
Abundance in Group 1: increased abundance in Deep Brain Stimulation DAT patients (t = 0 to t = 12)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Prevotella |
Revision editor(s): Bolanle, Fiddyhamma, WikiWorks
Experiment 11
Curated date: 2025/01/23
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Household Control (HC) at (t=0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease (PD) patients at (t=0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson disease patients on existing therapy regimes at (t=0)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 74
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Genus taxonomic level, at the t = 0
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Firmicutes bacterium CAG:56 | ||
| Fusicatenibacter | ||
| Erysipelotrichaceae UCG 003Erysipelotrichaceae UCG 003 | ||
| Lachnospiraceae ND3007 groupLachnospiraceae ND3007 group |
Revision editor(s): Fiddyhamma, Svetlana up, WikiWorks
Experiment 12
Curated date: 2025/01/23
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Household Control (HC) at (t=6)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease (PD) patients at (t=6)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson disease patients on existing therapy regimes at (t=6)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Genus taxonomic level, at the t = 6
Abundance in Group 1: decreased abundance in
Revision editor(s): Fiddyhamma, Svetlana up, WikiWorks
Experiment 13
Curated date: 2025/01/25
Curator:
Revision editor(s):
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Family taxonomic level, at the t = 6
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Enterobacteriaceae |
Revision editor(s): Fiddyhamma, WikiWorks
Signature 2
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Family taxonomic level, at the t = 6
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccaceae |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 14
Curated date: 2025/01/27
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Household Control (HC) at (t=12)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease (PD) patients at (t=12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson disease patients on existing therapy regimes at (t=12)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 2B
Description: Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Genus taxonomic level, at the t = 12
Abundance in Group 1: decreased abundance in
Revision editor(s): Fiddyhamma, Svetlana up, WikiWorks
