Gut microbiota in Parkinson’s disease patients: hospital-based study
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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
Parkinson’s disease (PD) is one of the most common neurodegenerative diseases. There is accumulating evidence that link gut microbiota to symptomatology and pathophysiology of PD. The aim of this study was to describe the pattern of gut microbiota and its association with PD and identify the effect of environmental factors on gut microbiota. This case–control study included 46 patients diagnosed as Parkinson’s disease (PD) and 31 healthy volunteers age and sex matched. Detailed history including age of onset, duration of disease, environmental risk factors, diet data, treatment, Unified Parkinson’s Disease Rating Scale (UPDRS), and gastrointestinal tract (GIT) domain of Non‐Motor Symptoms Scale (NMSS) were assessed. After extraction of bacterial DNA from the fecal samples, bacterial abundance was quantified by qPCR using 16S rRNA group-specific primers.
Results
Significant high abundance of Clostridium cluster IV, Akkermansia, Bifidobacterium, and lactic acid bacteria were found in the PD group compared with the control group (P < 0.001, 0.04, 0.02 and < 0.001, respectively), while Firmicutes were significantly less abundant in the PD group (P < 0.001) compared with the control group. The naive PD patients had significant abundance of Bifidobacterium, and lactic acid compared with control group. Interestingly, Akkermansia was more abundant in treated than untreated patients. There were significant associations between pesticide exposure and Bifidobacterium (P = 0.002), while no significant correlations between different gut microbiota and demographic, environment data, different rating scores or dominant type of PD. There was a significant negative correlation between the Bifidobacterium with the duration of illness (P = 0.012).
Conclusion
The present study highlighted a significant connection between PD and levels of certain types of gut microbiota, in support of a possible link between gut microbiota and a neurodegenerative cascade of PD.
Experiment 1
Subjects
- Location of subjects
- Egypt
- 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 relatives
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with parkinson's disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
- 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
- Not specified
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Source: Table 2
Description: Increased copy number of gut microbiota among Total Parkinson’s disease patients and control group
Abundance in Group 1: increased abundance in Parkinson's disease patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bifidobacterium | ||
| Clostridium cluster IVClostridium cluster IV | ||
| Lactic acid bacteriaLactic acid bacteria |
Revision editor(s): Karima
Signature 2
Source: Table 2
Description: Decreased copy number of gut microbiota among Total Parkinson’s disease patients and control group
Abundance in Group 1: decreased abundance in Parkinson's disease patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Karima
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Treated PD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with parkinson's disease under treatments
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Increased copy number of gut microbiota among treated PD patients versus control
Abundance in Group 1: increased abundance in Treated PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bifidobacterium | ||
| Clostridium cluster IVClostridium cluster IV | ||
| Lactic acid bacteriaLactic acid bacteria |
Revision editor(s): Karima
Signature 2
Source: Table 2
Description: Decreased copy number of gut microbiota among treated PD patients versus control
Abundance in Group 1: decreased abundance in Treated PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Karima
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Newly PD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Newly diagnosed patients with parkinson's disease ( non-treated patients)
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Increased copy number of gut microbiota among Newly diagnosed PD patients and control group
Abundance in Group 1: increased abundance in Newly PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Lactic acid bacteriaLactic acid bacteria |
Revision editor(s): Karima
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Newly PD patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Treated PD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients under treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Increased copy number of gut microbiota among treated PD patients and non-treated patients
Abundance in Group 1: increased abundance in Treated PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Karima
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD patients non exposed to pesticide
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients exposed to pesticide
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients exposed to pesticide
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Signature 1
Source: Table 4
Description: Correlation between gut microbiota and pesticide exposure in PD
Abundance in Group 1: decreased abundance in PD patients exposed to pesticide
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Karima
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD patients without constipation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD patients with constipation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease Patients with constipation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Source: Table 4
Description: Correlation between gut microbiota and constipation in Parkinson’s disease
Abundance in Group 1: increased abundance in PD patients with constipation
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Karima
