Oral and gut dysbiosis leads to functional alterations in Parkinson's disease/Experiment 3
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
- 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 symptom measurement Parkinson's disease symptom measurement,parkinson's disease symptom measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with mild Parkinson's disease (mild PD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with severe Parkinson's disease (severe PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients whose H&Y scale stage was 3 or greater.
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-3
Source: Supplementary figure 3b
Description: Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis.
Abundance in Group 1: increased abundance in Patients with severe Parkinson's disease (severe PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Cellulosilyticum | ||
| Coprococcus | ||
| Escherichia | ||
| Klebsiella | ||
| Lactobacillus | ||
| Olsenella | ||
| Proteus | ||
| PAC000745PAC000745 | ||
| AF349416AF349416 |
Revision editor(s): Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-3
Source: Supplementary figure 3b
Description: Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: decreased abundance in Patients with severe Parkinson's disease (severe PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Anaerotignum | ||
| Blautia | ||
| Eubacterium | ||
| Lachnospira | ||
| Eubacterium_g5Eubacterium_g5 | ||
| FR888536FR888536 | ||
| PAC000195PAC000195 | ||
| PAC000672PAC000672 | ||
| PAC000740PAC000740 |
Revision editor(s): Idiaru angela
