Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-3-3
Subjects
- Location of subjects
- Canada
- 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 (Ctrl)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson’s disease patients (PD patients)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 176
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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).
- centered log-ratio
- Statistical test
- Kruskall-Wallis
- MaAsLin2
- ANCOM-BC
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, sequence read depth, Confounders controlled for: "laxative use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.laxative use
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-3
Source: Fig. 2A
Description: Differentially abundance of species between healthy controls and PD patients using ANCOM-BC, MaAsLin2, and ALDEx2 (after controlling for confounders).
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus catus | ||
| Ruthenibacterium lactatiformans | ||
| Alistipes indistinctus | ||
| Blautia obeum |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-3
Source: Fig. 2A
Description: Differentially abundance of species between healthy controls and PD patients using ANCOM-BC, MaAsLin2, and ALDEx2 (after controlling for confounders).
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia inulinivorans | ||
| Roseburia intestinalis | ||
| Blautia wexlerae |
Revision editor(s): KateRasheed
