Dysbiosis of gut microbiota in a selected population of Parkinson's patients/Experiment 1
Curated date: 2024/03/08
Curator: Mojisayo Awolesi
Revision editor(s): Mojisayo Awolesi, Fiddyhamma, Scholastica
Subjects
- Location of subjects
- Italy
- 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 (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with severe and active Parkinson disease. Recruited patients had a diagnosis of idiopathic PD according to the UK Parkinson's Disease Society Brain Bank criteria with a disease duration (measured as the time following the first diagnosis) longer than 6 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 72
- Group 1 sample size Number of subjects in the case (exposed) group
- 80
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Linear Regression
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "loss of weight" 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.loss of weight
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Curated date: 2024/03/08
Curator: Mojisayo Awolesi
Revision editor(s): Scholastica, Fiddyhamma, Mojisayo Awolesi, Welile
Source: Supplementary Table S7A
Description: Significantly abundant bacterial families and genera in Parkinson's disease versus healthy controls (HC) detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test)
Abundance in Group 1: increased abundance in Parkinson's disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter | ||
| Enterobacteriaceae | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Klebsiella | ||
| Lactobacillaceae | ||
| Lactococcus | ||
| Salmonella | ||
| Shigella | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Scholastica, Fiddyhamma, Mojisayo Awolesi, Welile
Signature 2
Curated date: 2024/03/08
Curator: Mojisayo Awolesi
Revision editor(s): Scholastica, Fiddyhamma, Mojisayo Awolesi, Welile
Source: Supplementary Table S7A
Description: Significantly abundant bacterial families and genera in Parkinson's disease versus healthy controls (HC) detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test)
Abundance in Group 1: decreased abundance in Parkinson's disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Roseburia |
Revision editor(s): Scholastica, Fiddyhamma, Mojisayo Awolesi, Welile
