Analysis of the Gut Microflora in Patients With Parkinson's Disease
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B, Alkasir R
Journal
Frontiers in neuroscience
Year
2019
Keywords:
16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora
This study was conducted to explore the composition of the fecal microflora of Chinese Parkinson's disease (PD) patients, as well as to explore links between PD clinical features and antiparkinsonian medications on the gut microflora. Seventy-two PD cases [59 patients suffering from PD for >1 year (OPD) and 13 new PD (NPD) patients] were studied. Microflora communities in the feces of the patients and corresponding healthy controls (HCs) were examined using high-throughput Illumina MiSeq sequencing targeting the 16S rRNA gene. The gut microflora of OPD patients contained high levels of Rikenellaceae compared to corresponding HCs. In addition, significantly higher levels of Turicibacteraceae were found in the NPD group compared to the corresponding HCs. The genera Turicibacter and Prevotella were significantly correlated with the PD severity scores. Our findings that some fecal microflora were closely related to PD clinical characteristics may enhance our understanding of the pathogenesis and treatment of PD.
Experiment 1
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
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 without any form of Parkinson's Disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 68
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- The use of any antibiotics or probiotics within 90 days before collection of the samples.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Metastats
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, life style
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
Source: Figure 3. Genus level comparison among NPD samples.
Description: Genus-level comparison among NPD samples collected at different times.
Abundance in Group 1: increased abundance in NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Signature 2
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
Source: FIGURE 3
Description: Genus-level comparison among NPD samples collected at different times.
Abundance in Group 1: decreased abundance in NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.
| NCBI | Quality Control | Links |
|---|---|---|
| Paraprevotella | ||
| Ruminococcus | ||
| Streptococcus |
Experiment 2
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
Differences from previous experiment shown
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 5 days after treatment.
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
Source: FIGURE 3.
Description: Genus-level comparison among NPD samples collected at different times.
Abundance in Group 1: increased abundance in NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Experiment 3
Reviewed Marked as Reviewed by Lwaldron on 2022/07/1
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
Source: FIGURE 3.
Description: Genus-level comparison among NPD samples collected at different times.
Abundance in Group 1: increased abundance in NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Signature 2
Reviewed Marked as Reviewed by Rimsha on 2022/03/2
Source: FIGURE 3.
Description: Genus-level comparison among NPD samples collected at different times.
Abundance in Group 1: decreased abundance in NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus |
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