Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-8

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

34650532

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2021.728479

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8506127/

Authors

Mao L, Zhang Y, Tian J, Sang M, Zhang G, Zhou Y, Wang P

Journal

Frontiers in microbiology

Year

2021

Keywords:

Parkinson’s disease, gastrointestinal dysbiosis, gut-brain-axis, short-chain fatty acids, shotgun metagenomic sequencing

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson's disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid-related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-8

Curated date: 2023/05/31

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin, Peace Sandy

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 spouses

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: Partcipants with Parkinson's Disease

Group 0 sample size Number of subjects in the control (unexposed) group: 39

Group 1 sample size Number of subjects in the case (exposed) group: 39

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: WMS

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: BGISEQ-500 Sequencing

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)?: No

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: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-8

Curated date: 2023/05/31

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin, Peace Sandy

Source: Figure 2A and 2B

Description: The stool microbiota profile in PD and SP groups. Differential abundance of genera (A) and species (B) between PD and SP groups identified by LEfSe

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

NCBI	Quality Control	Links
Alistipes
Alistipes ihumii AP11
Alistipes indistinctus
Alistipes putredinis
Anaerotruncus
Anaerotruncus colihominis
Bifidobacterium dentium
Bilophila
Bilophila wadsworthia
Blautia hydrogenotrophica
Butyricimonas
Butyricimonas synergistica
Butyrivibrio
Clostridiales bacterium 1_7_47FAA
Desulfovibrio
Enterocloster asparagiformis
Enterocloster citroniae
Erysipelotrichaceae bacterium 21_3
Erysipelotrichaceae bacterium 2_2_44A
Eubacteriales
Hungatella hathewayi
Lachnospiraceae bacterium 3_1_57FAA_CT1
Lactobacillus gasseri
Leuconostoc pseudomesenteroides
Ligilactobacillus salivarius
Oscillibacter sp. KLE 1728
Oxalobacter
Oxalobacter formigenes
Parabacteroides goldsteinii
Rothia dentocariosa
Scardovia
Scardovia inopinata
Scardovia wiggsiae
Subdoligranulum
Subdoligranulum sp. 4_3_54A2FAA
Subdoligranulum variabile
[Clostridium] hylemonae
unclassified Bilophila
unclassified Olsenella
unclassified Scardovia
unclassified Subdoligranulum

Revision editor(s): Jacquelynshevin, Peace Sandy

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-8

Curated date: 2023/05/31

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin, Peace Sandy

Source: Figure 2A and 2B

Description: The stool microbiota profile in PD and SP groups. Differential abundance of genera (A) and species (B) between PD and SP groups identified by LEfSe

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

NCBI	Quality Control	Links
Bacteroides
Bacteroides sp. 3_1_19
Clostridium sp. L2-50
Eggerthia
Eggerthia catenaformis
Fusobacterium varium
Gemella haemolysans
Lachnospiraceae bacterium 9_1_43BFAA
Oscillospiraceae
Phocaeicola coprocola
Ruminococcaceae bacterium D16
Streptococcus pasteurianus
[Clostridium] leptum
[Clostridium] symbiosum
candidate division TM7 single-cell isolate TM7b
unclassified Peptostreptococcaceae
unclassified Sutterellaceae

Revision editor(s): Jacquelynshevin, Peace Sandy