Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-30
Curated date: 2021/11/14
Curator: Fcuevas3
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Fcuevas3, Atrayees, Aiyshaaaa
Subjects
- Location of subjects
- Germany
- 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 men without Parkinsons's Disease.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Men with Parkinson's Disease.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Only early stage PD men who were naïve to L-DOPA therapy as diagnosed according to the UK Brain Bank criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- The use of antibiotics in the past three months in principle was an exclusion criterion. However, we included three PD patients and three controls despite the intake of antibiotics for one to three days in a period of 28–34 days prior to feces sampling as the omission of those cases from the analyses did not change any result
Lab analysis
- Sequencing type
- 16S
- 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).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-30
Source: Figure 1C
Description: Differential microbial abundance between PD participants and controls
Abundance in Group 1: increased abundance in Men with Parkinson's Disease.
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Alistipes shahii | ||
| Lacrimispora saccharolytica | ||
| unclassified Bacillota | ||
| unclassified Bacteria | ||
| Eubacterium sp. | ||
| unclassified Clostridia |
Revision editor(s): Fcuevas3, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-30
Source: Figure 1C
Description: Differential microbial abundance between PD participants and controls
Abundance in Group 1: decreased abundance in Men with Parkinson's Disease.
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemanella biformis | ||
| Segatella copri |
Revision editor(s): Fcuevas3, Claregrieve1
