Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to Blautia Genus: Evidence From Feces, Blood, and Brain
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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
Guo X, Tang P, Hou C, Chong L, Zhang X, Liu P, Chen L, Liu Y, Zhang L, Li R
Journal
Frontiers in microbiology
Year
2022
Keywords:
16S, Blautia, Parkinson’s disease, feces, microbiome
A link between the gut microbiome and Parkinson's disease (PD) has been intensively studied, and more than 100 differential genera were identified across the studies. However, the predominant genera contributing to PD remain poorly understood. Inspired by recent advances showing microbiota distribution in the blood and brain, we, here, comprehensively investigated currently available fecal microbiome data (1,914 samples) to identify significantly altered genera, which were further validated by comparison to the results from microbiome analysis of blood (85 samples) and brain (268 samples). Our data showed that the composition of fecal microbiota was different from that of blood and brain. We found that Blautia was the unique genus consistently depleted across feces, blood, and brain samples of PD patients (P < 0.05), despite using rigorous criteria to remove contaminants. Moreover, enrichment analyses revealed that host genes correlated with Blautia genus abundance were mainly involved in mitochondrial function and energy metabolism, and mapped to neurodegenerative diseases (NDDs) and metabolic diseases. A random forest classifier constructed with fecal microbiota data demonstrated that Blautia genus was an important feature contributing to discriminating PD patients from controls [receiver operating characteristic (ROC)-area under curve (AUC) = 0.704, precision-recall curve (PRC)-AUC = 0.787]. Through the integration of microbiome and transcriptome, our study depicted microbial profiles in the feces, blood, and brain of PD patients, and identified Blautia genus as a potential genus linked to PD. Further studies are greatly encouraged to determine the role of Blautia genus in the pathogenesis of PD.
Experiment 1
Subjects
- 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
- 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
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1028
- Group 1 sample size Number of subjects in the case (exposed) group
- 1441
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, Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Supplementary Tables 4 and 5
Description: Significantly changed genera and species between PD patients and controls
Abundance in Group 1: increased abundance in PD patients
Revision editor(s): Leenaa
Signature 2
Source: Supplementary Tables 4 and 5
Description: Significantly changed genera between PD patients and controls
Abundance in Group 1: decreased abundance in PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Bacteroides | ||
| Blautia | ||
| Dorea | ||
| Faecalibacterium | ||
| Lachnospira | ||
| Phascolarctobacterium | ||
| Prevotella | ||
| Roseburia | ||
| Sutterella | ||
| rc4-4rc4-4 |
Revision editor(s): Leenaa
Experiment 2
Differences from previous experiment shown
Subjects
- Location of subjects
- China
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Blood Portion of blood,Vertebrate blood,Whole blood,Blood,blood
- Group 0 sample size Number of subjects in the control (unexposed) group
- 90
- Group 1 sample size Number of subjects in the case (exposed) group
- 90
Lab analysis
- 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
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
Source: Supplementary Table 6
Description: Significantly changed genera in the blood samples between PD patients and controls
Abundance in Group 1: decreased abundance in PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Dorea | ||
| Meiothermus | ||
| Nesterenkonia |
Revision editor(s): Leenaa
Experiment 3
Differences from previous experiment shown
Subjects
- Location of subjects
- Israel
- Netherlands
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Brain Encephalon,Suprasegmental levels of nervous system,Suprasegmental structures,Synganglion,The brain,Brain,brain
- Group 0 sample size Number of subjects in the control (unexposed) group
- 119
- Group 1 sample size Number of subjects in the case (exposed) group
- 150
Lab analysis
- Sequencing type
- Not specified
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3
Description: Significantly changed genera in the brain between PD patients and controls
Abundance in Group 1: increased abundance in PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Cronobacter | ||
| Nocardioides | ||
| Planctomyces | ||
| Rathayibacter | ||
| Syntrophobacter |
Revision editor(s): Leenaa
Signature 2
Source: Figure 3
Description: Significantly changed genera in the brain between PD patients and controls
Abundance in Group 1: decreased abundance in PD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia | ||
| Elizabethkingia | ||
| Erythrobacter | ||
| Finegoldia | ||
| Halomonas | ||
| Pseudonocardia | ||
| Thermoanaerobacterium |
Revision editor(s): Leenaa
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