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
- Treatment Treatment,treatment
- 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
- Jejunal 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 taxa in the vehicle group (VH) versus dopamine treatment group (D)
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 taxa in the vehicle group (VH) versus dopamine treatment group (D)
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
- Jejunal 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 taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group
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 taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group
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
- Jejunal 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 taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group
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 taxa in the vehicle group (VH) versus dopamine treatment group (D)
Abundance in Group 1: increased abundance in Dopamine treatment group (D)
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Firmicutes bacterium CAG_194_44_15 | ||
| Lachnospiraceae | ||
| Lachnospiraceae bacterium NK4A136 | ||
| Lactobacillus | ||
| 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 taxa in the vehicle group (VH) versus dopamine treatment group (D)
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 taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group
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 taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group
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 taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group
Abundance in Group 1: increased abundance in Ropinirole treatment group (R)
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Ileibacterium | ||
| 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 taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group
Abundance in Group 1: decreased abundance in Ropinirole treatment group (R)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium NK4A136 | ||
| Muribaculaceae | ||
| Roseburia | ||
| uncultured Lachnospiraceae bacterium | ||
| Ruminiclostridium_5Ruminiclostridium_5 |
Revision editor(s): Scholastica
