Gut microbiota in patients with Parkinson's disease in southern China
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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.
Authors
Lin A, Zheng W, He Y, Tang W, Wei X, He R, Huang W, Su Y, Huang Y, Zhou H, Xie H
Journal
Parkinsonism & related disorders
Year
2018
Keywords:
16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease
INTRODUCTION: Accumulating evidence has revealed alterations in the communication between the gut and brain in patients with Parkinson's disease (PD), and previous studies have confirmed that alterations in the gut microbiome play an important role in the pathogenesis of numerous diseases, including PD. The aim of this study was to determine whether the faecal microbiome of PD patients in southern China differs from that of control subjects and whether the gut microbiome composition alters among different PD motor phenotypes. METHODS: We compared the gut microbiota composition of 75 patients with PD and 45 age-matched controls using 16S rRNA next-generation-sequencing. RESULTS: We observed significant increases in the abundance of four bacterial families and significant decreases in the abundance of seventeen bacterial families in patients with PD compared to those of the controls. In particular, the abundance of Lachnospiraceae was reduced by 42.9% in patients with PD, whereas Bifidobacteriaceae was enriched in patients with PD. We did not identify a significant difference in the overall microbial composition among different PD motor phenotypes, but we identified the association between specific taxas and different PD motor phenotypes. CONCLUSIONS: PD is accompanied by alterations in the abundance of specific gut microbes. The abundance of certain gut microbes was altered depending on clinical motor phenotypes. Based on our findings, the gut microbiome may be a potential PD biomarker.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2023-3-10
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
- Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patient diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- 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)
- .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
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 2
Description: Specific microbial differences in taxa between PD and control in LEFSe and its adjusted P values.
Abundance in Group 1: increased abundance in Parkinson's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcaceae | ||
| Bifidobacteriaceae | ||
| Desulfovibrionaceae | ||
| Eubacteriaceae |
Revision editor(s): Jacquelynshevin
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 2
Description: Specific microbial differences in taxa between PD and control in LEFSe and its adjusted P values.
Abundance in Group 1: decreased abundance in Parkinson's disease
Revision editor(s): Jacquelynshevin, Aleru002
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD duration less than 5 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD duration more than 5 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with PD were classified into two groups according to disease duration: at least five years and less than five years.. Patients with PD were diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 3
Description: Taxa identified as significant difference between clinical phenotypes.
Abundance in Group 1: increased abundance in PD duration more than 5 years
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Deferribacteraceae | ||
| Mucispirillum | ||
| Rikenellaceae |
Revision editor(s): Jacquelynshevin
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 3
Description: Taxa identified as significant difference between clinical phenotypes.
Abundance in Group 1: decreased abundance in PD duration more than 5 years
| NCBI | Quality Control | Links |
|---|---|---|
| Phyllobacterium |
Revision editor(s): Jacquelynshevin
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Late-onset PD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early-onset PD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patient with age of onset less than 50.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 3
Description: Taxa identified as significant difference between clinical phenotypes.
Abundance in Group 1: increased abundance in Early-onset PD
| NCBI | Quality Control | Links |
|---|---|---|
| Alcaligenaceae | ||
| Facklamia | ||
| Faecalibacterium | ||
| Haemophilus | ||
| Lactococcus | ||
| Sutterella | ||
| Pasteurellaceae | ||
| Clostridium |
Revision editor(s): Jacquelynshevin
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 3
Description: Taxa identified as significant difference between clinical phenotypes.
Abundance in Group 1: decreased abundance in Early-onset PD
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Comamonas |
Revision editor(s): Jacquelynshevin
Experiment 4
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-tremor dominant PD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tremor dominant PD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patient with tremor dominant motor symptoms.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 56
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 3
Description: Taxa identified as significant difference between clinical phenotypes.
Abundance in Group 1: increased abundance in Tremor dominant PD
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Leptotrichiaceae |
Revision editor(s): Jacquelynshevin
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-10
Source: Table 3
Description: Taxa identified as significant difference between clinical phenotypes.
Abundance in Group 1: decreased abundance in Tremor dominant PD
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia |
Revision editor(s): Jacquelynshevin
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