Dysbiosis of gut microbiota in a selected population of Parkinson's patients
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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
Pietrucci D, Cerroni R, Unida V, Farcomeni A, Pierantozzi M, Mercuri NB, Biocca S, Stefani A, Desideri A
Journal
Parkinsonism & related disorders
Year
2019
Keywords:
16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors
INTRODUCTION: In recent years the hypothesis that gut microbiota associates with Parkinson's disease (PD) has gained importance, although it has not been possible to define a specific microbiota composition as a predictive biomarker of this disease. We have investigated dysbiosis of gut microbiota in a selected population of PD patients from Central Italy, and examined the weight of specific confounders and predictors, in order to identify potential correlations with clinical phenotypes. METHODS: 152 fecal samples were collected from 80 patients and 72 healthy controls. Patients were enrolled according to tight inclusion criteria. Microbiota composition was studied through 16s ribosomal RNA gene amplicon sequencing analysis in combination with data on dietary/life habits. Age, loss of weight, and sex were recognized as confounding factors, whereas PD-status, age, Body Mass Index, "eat cereals", "gain of weigth" and "physical activity" as predictors. The presence of Lactobacillaceae, Enterobacteriaceae and Enterococcaceae families was significantly higher in feces from PD patients compared to healthy controls, while Lachnospiraceae were significantly reduced. Lower levels of Lachnospiraceae and higher levels of Enterobacteriaceae families also correlated with increased disease severity and motor impairment (Hoehn & Yahr stage, MDS-UPDRS Part III). Predictive metagenomics indicated a significant variation of genes involved in the metabolism of short chain fatty acids and amino acids, and in lipopolysaccharide biosynthesis. CONCLUSIONS: PD showed a distinctive microbiota composition. Functional predictions suggest changes in pathways favoring a pro-inflammatory environment in the gastrointestinal tract, and a reduction in the biosynthesis of amino acids acting as precursors of physiological transmitters.
Experiment 1
Needs review
Subjects
- Location of subjects
- Italy
- 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson Disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with severe and active Parkinson disease. Recruited patients had a diagnosis of idiopathic PD according to the UK Parkinson's Disease Society Brain Bank criteria with a disease duration (measured as the time following the first diagnosis) longer than 6 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 72
- Group 1 sample size Number of subjects in the case (exposed) group
- 80
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Linear Regression
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "loss of weight" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.loss of weight
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
Needs review
Curated date: 2024/03/08
Curator: Mojisayo Awolesi
Revision editor(s): Mojisayo Awolesi, Welile, Fiddyhamma
Source: Table1A, Figure 1, Suppl table S7A and text
Description: PD cases vs HC, both bacterial Families and genera with a significative p-values detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test) are reported.
Abundance in Group 1: increased abundance in Parkinson Disease
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Enterococcaceae | ||
| Lactobacillaceae | ||
| Enterococcus | ||
| Lactococcus | ||
| Citrobacter | ||
| Klebsiella | ||
| Salmonella | ||
| Shigella | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Mojisayo Awolesi, Welile, Fiddyhamma
Signature 2
Needs review
Curated date: 2024/03/08
Curator: Mojisayo Awolesi
Revision editor(s): Mojisayo Awolesi, Welile, Fiddyhamma
Source: Table 1A, Figure 1, Suppl table S7A and text
Description: PD cases vs HC, both bacterial Families and genera with a significative p-values detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test) are reported.
Abundance in Group 1: decreased abundance in Parkinson Disease
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Roseburia |
Revision editor(s): Mojisayo Awolesi, Welile, Fiddyhamma
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson Disease (excluding patients taking iCOMT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with severe and active Parkinson’s disease taking catechol-O-methyl transferase (COMT) inhibitors are excluded from the analysis, since assumption of COMT inhibitors affects the microbiota composition
- Group 1 sample size Number of subjects in the case (exposed) group
- 72
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Table 1B, Fig 1, Suppl table S7B and text
Description: PD (excluding patients taking iCOMT) cases vs HC, both bacterial Families and genera with a significative p-values detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test) are reported.
Abundance in Group 1: increased abundance in Parkinson Disease (excluding patients taking iCOMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Lactobacillaceae | ||
| Enterococcaceae | ||
| Klebsiella | ||
| Lactobacillus | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Fiddyhamma
Signature 2
Needs review
Source: Table 1B, Fig 1, Suppl table S7B and text
Description: PD (excluding patients taking iCOMT) cases vs HC, both bacterial Families and genera with a significative p-values detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test) are reported.
Abundance in Group 1: decreased abundance in Parkinson Disease (excluding patients taking iCOMT)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae |
Revision editor(s): Fiddyhamma
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