Altered gut microbiota in Parkinson's disease patients/healthy spouses and its association with clinical features

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2023-3-7
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Zhang F, Yue L, Fang X, Wang G, Li C, Sun X, Jia X, Yang J, Song J, Zhang Y, Guo C, Ma G, Sang M, Chen F, Wang P
Journal
Parkinsonism & related disorders
Year
2020
Keywords:
Clinical features/classifications, Gut microbiota dysbiosis, Metagenomics, Neurodegenerative disease, Parkinson's disease (PD)
INTRODUCTION: Increasing evidence shows that gut microbiota dysbiosis may play important roles in the occurrence and progression of Parkinson's disease (PD), but the findings are inconsistent. Besides, the effect of family environment on gut microbiota dysbiosis remains unclear. METHODS: We characterized the gut microbial compositions of 63 PD patients, 63 healthy spouses (HS) and 74 healthy people (HP) using 16S rRNA sequencing. Clinical phenotypes and microbial composition were analyzed comprehensively. RESULTS: There were markedly different microbial compositions among PD, HS and HP samples by alpha/beta diversity. We also found differential microbial compositions among Hoehn & Yahr stage/disease duration. Eight inflammation-associated microbial genera shared a continuously increase trend with increased Hoehn & Yahr stage and disease duration, indicating characteristic bacteria associated with deterioration in PD. Additionally, seven bacterial markers were identified for accurately differentiating PD patients from the controls (area under the curve [AUC]: 0.856). CONCLUSIONS: Our study shows altered gut microbiota in PD patients. Importantly, inflammation-associated microbial genera may play roles in PD progression. Differential microbial compositions in HS and HP samples demonstrate that the gut microbiota are also affected by family environment. Disease-associated metagenomics studies should consider the family environmental factor. Our research provides an important reference and improves the understanding of gut microbiota in PD patients.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2023-3-7

Curated date: 2023/02/22

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin, Fatima

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
Healthy Controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Parkinson's Disease Patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The patients were diagnosed with primary Parkinson's disease according to the Movement Disorder Society Clinical Diagnostic Criteria for Parkinson’s disease (MDS-PD Criteria, 2015) of Xiangyang NO.1 People’s Hospital.
Group 0 sample size Number of subjects in the control (unexposed) group
137
Group 1 sample size Number of subjects in the case (exposed) group
63
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
90 days.

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).
raw counts
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

Alpha Diversity

Richness Number of species
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2023-3-7

Curated date: 2023/02/22

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin

Source: Table S2

Description: 33 significantly differential gut bacterial markers identified by LEfSe analysis.

Abundance in Group 1: increased abundance in Parkinson's Disease Patients

NCBI Quality ControlLinks
Deltaproteobacteria
Akkermansia
Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Clostridia
Desulfovibrionaceae
Desulfovibrionales
Escherichia
Lachnospiraceae
Oscillospira
Parabacteroides
Phascolarctobacterium
Porphyromonadaceae
Veillonellaceae
Verrucomicrobiaceae
Verrucomicrobiae
Verrucomicrobiales
Verrucomicrobiota
Oscillospiraceae
Eubacteriales
Bacillota
Pseudomonadota
Acidimicrobiia
Actinomycetes

Revision editor(s): Jacquelynshevin

Signature 2

Reviewed Marked as Reviewed by Fatima on 2023-3-7

Curated date: 2023/02/22

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin

Source: Table S2

Description: 33 significantly differential gut bacterial markers identified by LEfSe analysis.

Abundance in Group 1: decreased abundance in Parkinson's Disease Patients

NCBI Quality ControlLinks
Bacteroidales
Bacteroidia
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacterium
Fusobacteriota
Bacteroidota

Revision editor(s): Jacquelynshevin