Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-4-5
Subjects
- Location of subjects
- United States of America
- 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
- PC: healthy population controls without Parkinson's Disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD: Individuals with Parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale. cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 88
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 12 weeks
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- arcsine square-root
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- 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
- age, body mass index, race, sex
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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-4-5
Source: Figure 2 & figure S2
Description: Summary of differential abundance results contrasting healthy population controls and PD patients.
Abundance in Group 1: increased abundance in PD: Individuals with Parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Eisenbergiella | ||
| Eisenbergiella tayi | ||
| Ruthenibacterium | ||
| Ruthenibacterium lactatiformans |
Revision editor(s): Idiaru angela, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-4-5
Source: Figure 2 & figure S2
Description: Summary of differential abundance results contrasting healthy population controls and PD patients.
Abundance in Group 1: decreased abundance in PD: Individuals with Parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Firmicutes bacterium CAG:95 | ||
| Lachnospira eligens | ||
| Faecalibacterium | ||
| Butyrivibrio |
Revision editor(s): Idiaru angela, Folakunmi
