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
- 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
