Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15
Subjects
- Location of subjects
- India
- 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease from India
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- 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
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Nanopore
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)
- 0.01
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15
Source: Figure 5
Description: The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.
Abundance in Group 1: increased abundance in Parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Christensenellaceae | ||
| Oscillospiraceae |
Revision editor(s): Kaycee, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15
Source: Figure 5
Description: The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.
Abundance in Group 1: decreased abundance in Parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Coriobacteriaceae | ||
| Lachnospiraceae | ||
| Collinsella | ||
| Roseburia | ||
| Fusicatenibacter | ||
| Blautia | ||
| Faecalibacterium | ||
| Lachnospiraceae bacterium |
Revision editor(s): Kaycee, Peace Sandy
