The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- 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
- Duodenal mucosa Doudenal mucosa,Duodenal mucous membrane,Duodenum mucosa,Mucosa of duodenum,Mucous membrane of duodenum,Duodenal mucosa,duodenal 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's Disease (PD) Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 5c
Description: Taxa significantly abundant in the duodenal mucosal microbiota composition in control versus Parkinson's disease (PD) patients
Abundance in Group 1: increased abundance in Parkinson's Disease (PD) Patients
NCBI | Quality Control | Links |
---|---|---|
Burkholderiaceae | ||
Burkholderiales | ||
Gammaproteobacteria | ||
Lactococcus | ||
Massilia | ||
Oxalobacteraceae | ||
Pseudomonadota | ||
Ralstonia |
Revision editor(s): Scholastica
Signature 2
Source: Figure 5c
Description: Taxa significantly abundant in the duodenal mucosal microbiota composition in control versus Parkinson's disease (PD) patients
Abundance in Group 1: decreased abundance in Parkinson's Disease (PD) Patients
NCBI | Quality Control | Links |
---|---|---|
Flavobacteriaceae | ||
Rhodospirillales | ||
CAG56CAG56 |
Revision editor(s): Scholastica
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mucosa of sigmoid colon Mucosa of organ of sigmoid colon,Mucous membrane of sigmoid colon,Organ mucosa of sigmoid colon,Sigmoid colon mucosa,Sigmoid colon mucosa of organ,Sigmoid colon mucous membrane,Sigmoid colon organ mucosa,Mucosa of sigmoid colon,mucosa of sigmoid colon
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's Disease Patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 5d
Description: Taxa significantly abundant in the sigmoid mucosal microbiota composition in control versus Parkinson's disease (PD) patients
Abundance in Group 1: increased abundance in Parkinson's Disease Patients
NCBI | Quality Control | Links |
---|---|---|
Bifidobacterium longum | ||
Prevotellaceae |
Revision editor(s): Scholastica
Signature 2
Source: Figure 5d
Description: Taxa significantly abundant in the sigmoid mucosal microbiota composition in control versus Parkinson's disease (PD) patients
Abundance in Group 1: decreased abundance in Parkinson's Disease Patients
NCBI | Quality Control | Links |
---|---|---|
Thermoactinomycetaceae | ||
ThermoactinomycetalesThermoactinomycetales |
Revision editor(s): Scholastica
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Duodenal mucosa
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sigmoid mucosa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from the sigmoid mucosa of Parkinson's disease (PD) patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased