Colonic bacterial composition in Parkinson's disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-8-15
Subjects
- Location of subjects
- United States of America
- 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 control volunteers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's Disease subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- The use of probiotics or antibiotics within three months prior to sample collection.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V4
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)
- 0.05
Signature 1
Source: TABLE 1. Relative increased abundance of sequences derived from individual taxa
Description: Feces: Parkinson's disease vs. Healthy controls.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Bacteroidia | ||
| Clostridiaceae | ||
| Oscillospira | ||
| Pseudomonadota | ||
| Verrucomicrobiaceae | ||
| Verrucomicrobiota |
Signature 2
Source: TABLE 1. Relative decreased abundance of sequences derived from individual taxa
Description: Feces: Parkinson's Disease vs. Healthy Controls
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Blautia | ||
| Coprobacillaceae | ||
| Coprococcus | ||
| Dorea | ||
| Lachnospiraceae | ||
| Roseburia |
