Oral and gut dysbiosis leads to functional alterations in 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
Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW, Chung SJ
Journal
NPJ Parkinson's disease
Year
2022
Although several studies have identified a distinct gut microbial composition in Parkinson's disease (PD), few studies have investigated the oral microbiome or functional alteration of the microbiome in PD. We aimed to investigate the connection between the oral and gut microbiome and the functional changes in the PD-specific gut microbiome using shotgun metagenomic sequencing. The taxonomic composition of the oral and gut microbiome was significantly different between PD patients and healthy controls (P = 0.003 and 0.001, respectively). Oral Lactobacillus was more abundant in PD patients and was associated with opportunistic pathogens in the gut (FDR-adjusted P < 0.038). Functional analysis revealed that microbial gene markers for glutamate and arginine biosynthesis were downregulated, while antimicrobial resistance gene markers were upregulated in PD patients than healthy controls (all P < 0.001). We identified a connection between the oral and gut microbiota in PD, which might lead to functional alteration of the microbiome in PD.
Experiment 1
Needs review
Subjects
- Location of subjects
- South Korea
- 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
- Buccal mucosa Buccal mucosa,buccal mucosa
- 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 (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Parkinson's Disease (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics
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
- LEfSe
- 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
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 1f
Description: comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: increased abundance in Patients with Parkinson's Disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Mitsuokella | ||
| Alloscardovia | ||
| Capnocytophaga | ||
| Lactobacillus | ||
| Mogibacterium | ||
| Olsenella | ||
| Pseudoramibacter | ||
| Scardovia | ||
| Slackia |
Revision editor(s): Idiaru angela
Signature 2
Needs review
Source: figure 1f
Description: comparison of the oral microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: decreased abundance in Patients with Parkinson's Disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Lautropia | ||
| Oscillibacter | ||
| Sphingomonas | ||
| Mycoplasma_g17Mycoplasma_g17 | ||
| PAC000672PAC000672 | ||
| PAC001200PAC001200 |
Revision editor(s): Idiaru angela
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parkinson's disease symptom measurement Parkinson's disease symptom measurement,parkinson's disease symptom measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with mild Parkinson's disease (mild PD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with severe Parkinson's disease (severe PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease whose H&Y stage was 3 or greater
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Supplementary figure 3d
Description: Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: increased abundance in Patients with severe Parkinson's disease (severe PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Bifidobacterium | ||
| Capnocytophaga | ||
| Haemophilus | ||
| Lactobacillus | ||
| Olsenella | ||
| Pseudoramibacter | ||
| Scardovia | ||
| Eubacterium_g24Eubacterium_g24 |
Revision editor(s): Idiaru angela
Signature 2
Needs review
Source: Supplementary figure 3d
Description: Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: decreased abundance in Patients with severe Parkinson's disease (severe PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Lautropia |
Revision editor(s): Idiaru angela
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson's disease patients whose H&Y scale stage was 3 or greater.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Supplementary figure 3b
Description: Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis.
Abundance in Group 1: increased abundance in Patients with severe Parkinson's disease (severe PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Cellulosilyticum | ||
| Coprococcus | ||
| Escherichia | ||
| Klebsiella | ||
| Lactobacillus | ||
| Olsenella | ||
| Proteus | ||
| PAC000745PAC000745 | ||
| AF349416AF349416 |
Revision editor(s): Idiaru angela
Signature 2
Needs review
Source: Supplementary figure 3b
Description: Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis
Abundance in Group 1: decreased abundance in Patients with severe Parkinson's disease (severe PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Anaerotignum | ||
| Blautia | ||
| Eubacterium | ||
| Lachnospira | ||
| Eubacterium_g5Eubacterium_g5 | ||
| FR888536FR888536 | ||
| PAC000195PAC000195 | ||
| PAC000672PAC000672 | ||
| PAC000740PAC000740 |
Revision editor(s): Idiaru angela
Experiment 4
Needs review
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 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with Parkinson's Disease (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
- Group 1 sample size Number of subjects in the case (exposed) group
- 88
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- participants using antibiotics
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
- unchanged
Signature 1
Needs review
Source: figure 1e & text in paragraph 4, page 4
Description: Comparison of the gut microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: increased abundance in Patients with Parkinson's Disease (PD)
Revision editor(s): Idiaru angela
Signature 2
Needs review
Source: figure 1e
Description: Comparison of gut microbiome between PD and HCs using genus level LEfSe analysis.
Abundance in Group 1: decreased abundance in Patients with Parkinson's Disease (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Coprococcus | ||
| Enterococcus | ||
| Haemophilus | ||
| Prevotella | ||
| Roseburia | ||
| Ruminococcus | ||
| LLKBLLKB | ||
| PAC001043PAC001043 | ||
| PAC001032PAC001032 |
Revision editor(s): Idiaru angela
Experiment 5
Needs review
Differences from previous experiment shown
Subjects
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Participants using antibiotics.
Lab analysis
- Sequencing type
- WMS
- 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).
- raw counts
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 1
Needs review
Source: Figure 3c & paragraph 2, page 5
Description: Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.
Abundance in Group 1: increased abundance in Patients with Parkinson's Disease (PD)
Revision editor(s): Idiaru angela
Signature 2
Needs review
Source: Figure 3c
Description: Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.
Abundance in Group 1: decreased abundance in Patients with Parkinson's Disease (PD)
Revision editor(s): Idiaru angela
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