Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation
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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
- Constipation , Parkinson's disease Constipation,Costiveness,Dyschezia,constipation,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 Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients with constipation before FMT
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- 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
- Not specified
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
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Fig. 2C and 2D
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to the Health Control group (HC)
Abundance in Group 1: increased abundance in Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroidales | ||
| Bacteroides | ||
| Bacteroidia | ||
| Bacteroidota |
Revision editor(s): Ikehdarlington, ChiomaBlessing
Signature 2
Source: Fig. 2C and 2D
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to the Health Control group (HC)
Abundance in Group 1: decreased abundance in Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria | ||
| Burkholderiaceae | ||
| Clostridia | ||
| Enterobacteriaceae | ||
| Peptostreptococcaceae | ||
| Bacillota |
Revision editor(s): Ikehdarlington, ChiomaBlessing
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Parkinson's disease patients before fecal microbiota transplant (FMT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease patients after fecal microbiota transplant (FMT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients 12 weeks after FMT
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
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
- increased
Signature 2
Source: Fig. 2C and 2D
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 12 weeks after FMT
Abundance in Group 1: increased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
Revision editor(s): Ikehdarlington, ChiomaBlessing
Experiment 3
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
- 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
Signature 1
Source: Fig. 3B and 3D
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 12 weeks after FMT
Abundance in Group 1: decreased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Fig. 3C and 3E
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 12 weeks after FMT
Abundance in Group 1: increased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Faecalibacterium |
Revision editor(s): ChiomaBlessing
Experiment 4
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients 8 weeks after FMT
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 3B and 3D
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 8 weeks after FMT
Abundance in Group 1: decreased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Fig. 3E
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 8 weeks after FMT
Abundance in Group 1: increased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia |
Revision editor(s): ChiomaBlessing
Experiment 5
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients 4 weeks after FMT
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 3D
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 4 weeks after FMT
Abundance in Group 1: decreased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Fig. 3C
Description: Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 4 weeks after FMT
Abundance in Group 1: increased abundance in Parkinson's disease patients after fecal microbiota transplant (FMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium |
Revision editor(s): ChiomaBlessing
