Oral and gut dysbiosis leads to functional alterations 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
Curated date: 2024/03/29
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.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Buccal mucosa
- 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
- Healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Parkinson's Disease (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics
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)?
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 1f
Description: comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Mitsuokella | ||
| Alloscardovia | ||
| Capnocytophaga | ||
| Lactobacillus | ||
| Mogibacterium | ||
| Olsenella | ||
| Pseudoramibacter | ||
| Scardovia | ||
| Slackia |
Revision editor(s): Idiaru angela, WikiWorks
Signature 2
Source: figure 1f
Description: comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Lautropia | ||
| Oscillibacter | ||
| Sphingomonas | ||
| Mycoplasma_g17Mycoplasma_g17 | ||
| PAC000672PAC000672 | ||
| PAC001200PAC001200 |
Revision editor(s): Idiaru angela, WikiWorks
Experiment 2
Curated date: 2024/03/29
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parkinson's disease symptom measurement Parkinson's disease symptom measurement,parkinson's disease symptom measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with mild Parkinson's disease (mild PD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with severe Parkinson's disease (severe PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease whose H&Y stage was 3 or greater
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary figure 3d
Description: Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Bifidobacterium | ||
| Capnocytophaga | ||
| Haemophilus | ||
| Lactobacillus | ||
| Olsenella | ||
| Pseudoramibacter | ||
| Scardovia | ||
| Eubacterium_g24Eubacterium_g24 |
Revision editor(s): Idiaru angela, WikiWorks
Signature 2
Source: Supplementary figure 3d
Description: Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Lautropia |
Revision editor(s): Idiaru angela, WikiWorks
Experiment 3
Curated date: 2024/03/29
Curator:
Revision editor(s):
Subjects
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients whose H&Y scale stage was 3 or greater.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary figure 3b
Description: Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Cellulosilyticum | ||
| Coprococcus | ||
| Escherichia | ||
| Klebsiella | ||
| Lactobacillus | ||
| Olsenella | ||
| Proteus | ||
| PAC000745PAC000745 | ||
| AF349416AF349416 |
Revision editor(s): Idiaru angela, WikiWorks
Signature 2
Source: Supplementary figure 3b
Description: Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Anaerotignum | ||
| Blautia | ||
| Eubacterium | ||
| Lachnospira | ||
| Eubacterium_g5Eubacterium_g5 | ||
| FR888536FR888536 | ||
| PAC000195PAC000195 | ||
| PAC000672PAC000672 | ||
| PAC000740PAC000740 |
Revision editor(s): Idiaru angela, WikiWorks
Experiment 4
Curated date: 2024/03/29
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
- Healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Parkinson's Disease (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
- Group 1 sample size Number of subjects in the case (exposed) group
- 88
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: figure 1e & text in paragraph 4, page 4
Description: Comparison of the gut microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: increased abundance in
Revision editor(s): Idiaru angela, WikiWorks
Signature 2
Source: figure 1e
Description: Comparison of gut microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Coprococcus | ||
| Enterococcus | ||
| Haemophilus | ||
| Prevotella | ||
| Roseburia | ||
| Ruminococcus | ||
| LLKBLLKB | ||
| PAC001043PAC001043 | ||
| PAC001032PAC001032 |
Revision editor(s): Idiaru angela, WikiWorks
Experiment 5
Curated date: 2024/03/30
Curator:
Revision editor(s):
Subjects
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 3c & paragraph 2, page 5
Description: Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.
Abundance in Group 1: increased abundance in
Revision editor(s): Idiaru angela, WikiWorks
Signature 2
Source: Figure 3c
Description: Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.
Abundance in Group 1: decreased abundance in
Revision editor(s): Idiaru angela, WikiWorks
