The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder
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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
Curated date: 2023/03/11
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Lwaldron, Fatima
Subjects
- Location of subjects
- Germany
- 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
- Nasal cavity Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity,nasal cavity
- 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
- Parkinson's Disease Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Curated date: 2023/03/11
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Source: Results of the differential analysis of the nasal microbiota
Description: Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: increased abundance in Parkinson's Disease Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Carnobacteriaceae | ||
| Hydrogenophilaceae | ||
| Hyphomicrobiaceae |
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Signature 2
Curated date: 2023/03/11
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Source: Results of the differential analysis of the nasal microbiota
Description: Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: decreased abundance in Parkinson's Disease Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillaceae | ||
| Bacillales incertae sedis | ||
| Desulfovibrionaceae | ||
| Listeriaceae | ||
| Micrococcaceae | ||
| Oscillospiraceae | ||
| Oxalobacteraceae |
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Experiment 2
Curated date: 2023/03/11
Curator: Jacquelynshevin
Revision editor(s): Fatima, Jacquelynshevin, Lwaldron
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- REM sleep behavior disorder Rapid eye movement sleep behavior disorder,rapid eye movement sleep behavior disorder,REM Sleep Behavior Disorder,REM sleep behavior disorder,rEM sleep behavior disorder
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- idiopathic rapid eye movement sleep behavior disorder
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2023/03/11
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Source: Results of the differential analysis of the nasal microbiota
Description: Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: decreased abundance in idiopathic rapid eye movement sleep behavior disorder
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales incertae sedis | ||
| Desulfovibrionaceae | ||
| Oxalobacteraceae |
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Experiment 3
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's Disease Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- intake of diabetes medication
Signature 1
Curated date: 2023/03/14
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Source: Summarized results of the differential and regression analyses of the gut microbiota
Description: Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: increased abundance in Parkinson's Disease Patients
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Signature 2
Curated date: 2023/03/14
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Source: Summarized results of the differential and regression analyses of the gut microbiota
Description: Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: decreased abundance in Parkinson's Disease Patients
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- REM sleep behavior disorder Rapid eye movement sleep behavior disorder,rapid eye movement sleep behavior disorder,REM Sleep Behavior Disorder,REM sleep behavior disorder,rEM sleep behavior disorder
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- idiopathic rapid eye movement sleep behavior disorder
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2023/03/14
Curator: Jacquelynshevin
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Source: Summarized results of the differential and regression analyses of the gut microbiota:
Description: Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: increased abundance in idiopathic rapid eye movement sleep behavior disorder
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Erysipelotrichaceae incertae sedis | ||
| Flavonifractor | ||
| Gordonibacter | ||
| Lachnospiraceae | ||
| Blautia coccoides |
Revision editor(s): Jacquelynshevin, Fatima, WikiWorks
Signature 2
Source: Summarized results of the differential and regression analyses of the gut microbiota
Description: Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.
Abundance in Group 1: decreased abundance in idiopathic rapid eye movement sleep behavior disorder
Revision editor(s): Jacquelynshevin, Fatima
