Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2024/03/16
Curator:
Revision editor(s):
Subjects
- Location of subjects
- South Korea
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MPTP Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).
- 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
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)
- 0.05
- 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
- 2.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4G
Description: Differences in bacterial taxa abundance in the MPTP Group (Mice treated with MPTP) VS Control group.
Abundance in Group 1: increased abundance in
Signature 2
Source: Figure 4G and 4F
Description: Differences in bacterial taxa abundance in the MPTP group (mice treated with MPTP) vs. the control group.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Amedibacillus dolichus | ||
| Amedibacterium |
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MPTP + Acu Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with MPTP received acupuncture.
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
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
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4G and 4F
Description: Differences in bacterial taxa abundance in the MPTP + Acu (Mice treated with MPTP that received Acupuncture) vs. Control group
Abundance in Group 1: increased abundance in MPTP + Acu Group
Signature 2
Source: Figure 4G and 4F
Description: Differences in bacterial taxa abundance in the MPTP + Acu (Mice treated with MPTP that received Acupuncture) vs. Control group
Abundance in Group 1: decreased abundance in MPTP + Acu Group
| NCBI | Quality Control | Links |
|---|---|---|
| Amedibacillus | ||
| Amedibacillus dolichus |
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- MPTP + Acu Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MPTP + Non Acu Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with MPTP did not receive acupuncture
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
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
- decreased
- Richness Number of species
- decreased
Experiment 5
Curated date: 2024/04/09
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MPTP group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).
- 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)
- N/A
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Curated date: 2024/04/09
Curator: MyleeeA
Revision editor(s): WikiWorks, ChiomaBlessing, MyleeeA, Mariposa
Source: Fig 5 and Supplementary Table S1
Description: Bacterial genera with significant differences in the gut microbiota of MPTP group VS Control group.
Abundance in Group 1: increased abundance in
Revision editor(s): WikiWorks, ChiomaBlessing, MyleeeA, Mariposa
Signature 2
Curated date: 2024/04/09
Curator: MyleeeA
Revision editor(s): WikiWorks, ChiomaBlessing, MyleeeA, Mariposa
Source: Figure 5 and Supplementary Table S1
Description: Bacterial genera with significant differences in the gut microbiota of MPTP group VS Control group.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Acutalibacter | ||
| Anaerotruncus | ||
| Butyricimonas | ||
| Desulfitobacterium | ||
| Dorea | ||
| Flintibacter | ||
| Gracilibacter | ||
| Merdimmobilis | ||
| Oscillibacter | ||
| Saccharofermentans |
Revision editor(s): WikiWorks, ChiomaBlessing, MyleeeA, Mariposa
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MPTP+Acu group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
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
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 5 and Supplementary Table S1
Description: Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS Control group.
Abundance in Group 1: increased abundance in MPTP+Acu group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Pseudoclostridium | ||
| Vallitalea | ||
| Vampirovibrio |
Revision editor(s): MyleeeA, ChiomaBlessing, WikiWorks
Signature 2
Source: Figure 5 and Supplementary Table S1
Description: Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS Control group.
Abundance in Group 1: decreased abundance in MPTP+Acu group
| NCBI | Quality Control | Links |
|---|---|---|
| Amedibacterium |
Revision editor(s): MyleeeA, ChiomaBlessing, WikiWorks
Experiment 7
Curated date: 2024/04/09
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- MPTP group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
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
- increased
- Richness Number of species
- increased
Signature 1
Curated date: 2024/04/09
Curator: MyleeeA
Revision editor(s): WikiWorks, ChiomaBlessing, MyleeeA, Mariposa
Source: Figure 5 and Supplementary Table S1
Description: Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS MPTP group.
Abundance in Group 1: increased abundance in
Revision editor(s): WikiWorks, ChiomaBlessing, MyleeeA, Mariposa
Signature 2
Source: Figure 5 and Supplementary Table S1
Description: Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS MPTP group.
Abundance in Group 1: decreased abundance in
Revision editor(s): MyleeeA, ChiomaBlessing, WikiWorks
