Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to Blautia Genus: Evidence From Feces, Blood, and Brain

From BugSigDB
Needs review
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


Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

Subjects

Location of subjects
China
Denmark
Finland
Germany
Italy
Japan
United States of America
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

Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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

NCBI Quality ControlLinks
Abiotrophia defectiva
Acidaminococcus
Anaerofustis
Anaerotruncus
Campylobacter
Citrobacter
Coprobacillus
Dehalobacterium
Eubacterium
Finegoldia
Gallicola
Halomonas
Methanobrevibacter
Methanomassiliicoccus
Mogibacterium
Pediococcus
Peptoniphilus
Proteus
Ruminococcus
Sporobacterium sp. WAL 1855D
Synergistes
Turicibacter
Varibaculum
unclassified Pediococcus
Pseudoramibacter_EubacteriumPseudoramibacter_Eubacterium
cc_115cc_115
1-681-68
ph2ph2

Revision editor(s): Leenaa

Signature 2

Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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 ControlLinks
Anaerostipes
Bacteroides
Blautia
Dorea
Faecalibacterium
Lachnospira
Phascolarctobacterium
Prevotella
Roseburia
Sutterella
rc4-4rc4-4

Revision editor(s): Leenaa

Experiment 2


Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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

Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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 ControlLinks
Blautia
Dorea
Meiothermus
Nesterenkonia

Revision editor(s): Leenaa

Experiment 3


Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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

Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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 ControlLinks
Cronobacter
Nocardioides
Planctomyces
Rathayibacter
Syntrophobacter

Revision editor(s): Leenaa

Signature 2

Needs review

Curated date: 2024/03/27

Curator: Leenaa

Revision editor(s): Leenaa

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 ControlLinks
Bacteroides
Blautia
Elizabethkingia
Erythrobacter
Finegoldia
Halomonas
Pseudonocardia
Thermoanaerobacterium

Revision editor(s): Leenaa