Oral and gut dysbiosis leads to functional alterations in Parkinson's disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-7-3
Subjects
- Location of subjects
- South Korea
- 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
- Buccal mucosa Buccal mucosa,buccal mucosa
- 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
- Patients with Parkinson's Disease (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics
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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-3
Source: Figure 1f
Description: comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: increased abundance in Patients with Parkinson's Disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Mitsuokella | ||
| Alloscardovia | ||
| Capnocytophaga | ||
| Lactobacillus | ||
| Mogibacterium | ||
| Olsenella | ||
| Pseudoramibacter | ||
| Scardovia | ||
| Slackia |
Revision editor(s): Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-3
Source: figure 1f
Description: comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: decreased abundance in Patients with Parkinson's Disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Lautropia | ||
| Oscillibacter | ||
| Sphingomonas | ||
| Mycoplasma_g17Mycoplasma_g17 | ||
| PAC000672PAC000672 | ||
| PAC001200PAC001200 |
Revision editor(s): Idiaru angela
