The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study
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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
- United Kingdom
- 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 Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Idiopathic Parkinson's Disease Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that either referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group) or reported stability of body weight from the diagnosis to the time of evaluation (NWL group).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
- 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
Signature 1
Source: Figure 1
Description: The most differentially enriched taxa in Parkinson’s disease patients (PARK) and CTRL groups. Computed Linear discriminant analysis (LDA) scores of the taxa relative abundance difference between the PARK and CTRL groups at phylum (A) and genus (B) levels. Positive LDA scores (green) are enriched in PARK group, while negative LDA scores (red) are enriched in CTRL.
Abundance in Group 1: increased abundance in Idiopathic Parkinson's Disease Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Oxalobacteraceae | ||
| Pseudomonadota |
Revision editor(s): Jacquelynshevin
Signature 2
Source: Figure 1
Description: Figure 1. The most differentially enriched taxa in Parkinson’s disease patients (PARK) and CTRL groups. Computed Linear discriminant analysis (LDA) scores of the taxa relative abundance difference between the PARK and CTRL groups at phylum (A) and genus (B) levels. Positive LDA scores (green) are enriched in PARK group, while negative LDA scores (red) are enriched in CTRL.
Abundance in Group 1: decreased abundance in Idiopathic Parkinson's Disease Patients
Revision editor(s): Jacquelynshevin, Folakunmi
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls and Idiopathic Parkinson's Disease Patients with Weight Loss
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Idiopathic Parkinson's Disease Patients without Weight Loss
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3
Description: The most differentially enriched taxa in non weight loss, weight loss and CTRL groups. Computed LDA scores of the relative abundance difference between the three groups. Positive LDA scores (red) are enriched in NWL group.
Abundance in Group 1: increased abundance in Idiopathic Parkinson's Disease Patients without Weight Loss
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): Jacquelynshevin
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Idiopathic Parkinson's Disease Patients with Weight Loss
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4A
Description: The most differentially enriched taxa in the CTRL versus weight loss comparison.
Abundance in Group 1: increased abundance in Idiopathic Parkinson's Disease Patients with Weight Loss
| NCBI | Quality Control | Links |
|---|---|---|
| Bilophila | ||
| Desulfovibrionaceae | ||
| Odoribacter | ||
| Oxalobacteraceae | ||
| unclassified Paraprevotella |
Revision editor(s): Jacquelynshevin, Folakunmi
Signature 2
Source: Figure 4A
Description: The most differentially enriched taxa in the CTRL versus weight loss comparison.
Abundance in Group 1: decreased abundance in Idiopathic Parkinson's Disease Patients with Weight Loss
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovorax | ||
| Bifidobacterium pseudolongum | ||
| Granulicatella | ||
| Actinomyces | ||
| Prevotellaceae | ||
| Atopobium | ||
| Anaerococcus | ||
| Planococcaceae |
Revision editor(s): Jacquelynshevin
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Idiopathic Parkinson's Disease Patients without Weight Loss
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4B
Description: The most differentially enriched taxa in the CTRL versus NWL comparison.
Abundance in Group 1: increased abundance in Idiopathic Parkinson's Disease Patients without Weight Loss
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Eggerthella lenta | ||
| Enterococcus | ||
| Candidatus Epulonipiscium |
Revision editor(s): Jacquelynshevin
Signature 2
Source: Figure 4B
Description: The most differentially enriched taxa in the CTRL versus NWL comparison.
Abundance in Group 1: decreased abundance in Idiopathic Parkinson's Disease Patients without Weight Loss
Revision editor(s): Jacquelynshevin, Folakunmi
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Idiopathic Parkinson's Disease Patients without Weight Loss
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Idiopathic Parkinson's Disease Patients with Weight Loss
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, time from diagnosis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4C
Description: The most differentially enriched taxa in the NWL versus weight loss comparison.
Abundance in Group 1: increased abundance in Idiopathic Parkinson's Disease Patients with Weight Loss
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae | ||
| Lachnospira | ||
| Ruminococcus bromii | ||
| Clostridiaceae | ||
| Peptococcaceae | ||
| Collinsella aerofaciens | ||
| Oscillospiraceae | ||
| Collinsella | ||
| Desulfovibrionaceae | ||
| Roseburia |
Revision editor(s): Jacquelynshevin
Signature 2
Source: Figure 4C
Description: The most differentially enriched taxa in the NWL versus weight loss comparison.
Abundance in Group 1: decreased abundance in Idiopathic Parkinson's Disease Patients with Weight Loss
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcaceae | ||
| Escherichia coli | ||
| Enterococcus | ||
| Eggerthella lenta | ||
| Faecalibacterium prausnitzii | ||
| Enterococcus cecorum | ||
| Enterobacteriaceae |
Revision editor(s): Jacquelynshevin
