Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats
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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
- Netherlands
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
- 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
- Vehicle group (VH)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dopamine treatment group (D)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Proximal small intestinal samples from rats treated for 14 sequential days with dopamine (D)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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
- 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)
- 0.01
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: increased abundance in Dopamine treatment group (D)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Pantoea agglomerans |
Revision editor(s): Adeitan, Scholastica
Signature 2
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: decreased abundance in Dopamine treatment group (D)
Revision editor(s): Adeitan, Welile, Scholastica
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pramipexole treatment group (P)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Proximal small intestinal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: increased abundance in Pramipexole treatment group (P)
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: decreased abundance in Pramipexole treatment group (P)
Revision editor(s): Scholastica
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ropinirole treatment group (R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Proximal small intestinal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: decreased abundance in Ropinirole treatment group (R)
Revision editor(s): Scholastica
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dopamine treatment group (D)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileal samples from rats treated for 14 sequential days with dopamine (D)
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: increased abundance in Dopamine treatment group (D)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lachnospiraceae | ||
| Allobaculum | ||
| Lachnospiraceae bacterium NK4A136 | ||
| Firmicutes bacterium CAG_194_44_15 | ||
| Oscillibacter | ||
| Oscillospiraceae | ||
| uncultured prokaryote |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: decreased abundance in Dopamine treatment group (D)
Revision editor(s): Scholastica
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pramipexole treatment group (P)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: increased abundance in Pramipexole treatment group (P)
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: decreased abundance in Pramipexole treatment group (P)
Revision editor(s): Scholastica
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ropinirole treatment group (R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: increased abundance in Ropinirole treatment group (R)
| NCBI | Quality Control | Links |
|---|---|---|
| Ileibacterium | ||
| Allobaculum | ||
| Lactobacillus | ||
| uncultured Erysipelotrichia bacterium |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Table S1
Description: Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant features with P value <0.01 and log(LDA score) >2.
Abundance in Group 1: decreased abundance in Ropinirole treatment group (R)
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Roseburia | ||
| Lachnospiraceae bacterium NK4A136 | ||
| Ruminiclostridium_5Ruminiclostridium_5 | ||
| uncultured Lachnospiraceae bacterium |
Revision editor(s): Scholastica
