Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson's Disease Cohort

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-7-1

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

34776854

DOI Digital object identifier for electronic documents.

10.3389/fnins.2021.756951

URI

Authors

Kenna JE, Chua EG, Bakeberg M, Tay A, McGregor S, Gorecki A, Horne M, Marshall B, Mastaglia FL, Anderton RS

Journal

Frontiers in neuroscience

Year

2021

Keywords:

16S, KEGG, Parkinson’s disease, gut bacteria, gut microbiome

Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson's disease (PD), but the influence of geographic location has received little attention. The present study characterized the gut microbiota and associated changes in host metabolic pathways in an Australian cohort of people with PD (PwP). Methods: The study involved recruitment and assessment of 87 PwP from multiple Movement Disorders Clinics in Australia and 47 healthy controls. Illumina sequencing of the V3 and V4 regions of the 16S rRNA gene was used to distinguish inter-cohort differences in gut microbiota; KEGG analysis was subsequently performed to predict functional changes in host metabolic pathways. Results: The current findings identified significant differences in relative abundance and diversity of microbial operational taxonomic units (OTUs), and specific bacterial taxa between PwP and control groups. Alpha diversity was significantly reduced in PwP when compared to controls. Differences were found in two phyla (Synergistetes and Proteobacteria; both increased in PwP), and five genera (Colidextribacter, Intestinibacter, Kineothrix, Agathobaculum, and Roseburia; all decreased in PwP). Within the PD cohort, there was no association identified between microbial composition and gender, constipation or use of gastrointestinal medication. Furthermore, KEGG analysis identified 15 upregulated and 11 downregulated metabolic pathways which were predicted to be significantly altered in PwP. Conclusion: This study provides the first comprehensive characterization of the gut microbiome and predicted functional metabolic effects in a southern hemisphere PD population, further exploring the possible mechanisms whereby the gut microbiota may exert their influence on this disease, and providing evidence for the incorporation of such data in future individualized therapeutic strategies.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-1

Curated date: 2024/03/13

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica

Subjects

Location of subjects: Australia

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: People with Parkinson's Disease (PWP)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: People with Parkinson's Disease from multiple Movement Disorders Clinics

Group 0 sample size Number of subjects in the control (unexposed) group: 47

Group 1 sample size Number of subjects in the case (exposed) group: 87

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: 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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Richness Number of species: decreased

Signature 1

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Curated date: 2024/03/18

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica

Source: Figure 2

Description: Significantly different taxa in the gut microbiome of controls compared to people with Parkinson's disease (PwP) following 16S rRNA sequencing.

Abundance in Group 1: increased abundance in People with Parkinson's Disease (PWP)

NCBI	Quality Control	Links
Enterobacteriaceae
Gammaproteobacteria
Synergistia
Pseudomonadota
Synergistota
Enterobacterales

Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2024-7-1

Curated date: 2024/03/18

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica

Source: Figure 2

Description: Significantly different taxa in the gut microbiome of controls compared to people with Parkinson's disease (PwP) following 16S rRNA sequencing.

Abundance in Group 1: decreased abundance in People with Parkinson's Disease (PWP)

NCBI	Quality Control	Links
Agathobaculum
Clostridiales bacterium
Colidextribacter
Intestinibacter
Kineothrix
Lachnospiraceae
Roseburia
Clostridia
Eubacteriales

Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica