Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China
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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
- 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
- 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(HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The patients who have been diagnosed with Parkinson's Disease(PD). Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by motor and non-motor symptoms.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3
Description: Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups
Abundance in Group 1: increased abundance in patients with parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Oscillospiraceae |
Signature 2
Source: Figure 3
Description: Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups.
Abundance in Group 1: decreased abundance in patients with parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Muribaculaceae |
Experiment 2
Subjects
- 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 subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2A. Phylum, increased abundances.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiota |
Revision editor(s): Fcuevas3
Signature 2
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2B. Class. Increased abundances.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Negativicutes | ||
| Verrucomicrobiia |
Revision editor(s): Fcuevas3
Signature 3
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2B. Class, decreased abundances.
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli |
Revision editor(s): Fcuevas3
Signature 4
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2C. Order, increased abundances.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Selenomonadales | ||
| Verrucomicrobiales |
Revision editor(s): Fcuevas3
Signature 5
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2C. Order, decreased abundances.
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillales |
Revision editor(s): Fcuevas3
Signature 6
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2D. Family, increased abundances.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcaceae | ||
| Oscillospiraceae | ||
| Porphyromonadaceae | ||
| Rikenellaceae | ||
| Veillonellaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Fcuevas3
Signature 7
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2D. Family, decreased abundances.
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Muribaculaceae |
Signature 8
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests
Description: 2E. Genus, increased abundances.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
Revision editor(s): Fcuevas3
Signature 9
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests
Description: 2E. Genus, decreased abundances.
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum hallii | ||
| Lactobacillus | ||
| Streptococcus |
Revision editor(s): Fcuevas3
Signature 10
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.
Description: 2F. Species, increased abundances.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobrevibacter smithii | ||
| Parabacteroides merdae | ||
| Segatella copri | ||
| Roseburia inulinivorans | ||
| Ruminococcus callidus | ||
| [Ruminococcus] torques |
Revision editor(s): Fcuevas3
Signature 11
Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests
Description: 2F. Species, decreased abundances.
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus gasseri |
Revision editor(s): Fcuevas3
