The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder/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
