Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

35645785

DOI Digital object identifier for electronic documents.

10.3389/fnagi.2022.881872

URI

Authors

Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL, Sue CM

Journal

Frontiers in aging neuroscience

Year

2022

Keywords:

Parkinson’s disease, biomarker, dysbiosis, gastrointestinal microbiome, gut microbiota, medication, prediction model

BACKGROUND: Models to predict Parkinson's disease (PD) incorporating alterations of gut microbiome (GM) composition have been reported with varying success. OBJECTIVE: To assess the utility of GM compositional changes combined with macronutrient intake to develop a predictive model of PD. METHODS: We performed a cross-sectional analysis of the GM and nutritional intake in 103 PD patients and 81 household controls (HCs). GM composition was determined by 16S amplicon sequencing of the V3-V4 region of bacterial ribosomal DNA isolated from stool. To determine multivariate disease-discriminant associations, we developed two models using Random Forest and support-vector machine (SVM) methodologies. RESULTS: Using updated taxonomic reference, we identified significant compositional differences in the GM profiles of PD patients in association with a variety of clinical PD characteristics. Six genera were overrepresented and eight underrepresented in PD patients relative to HCs, with the largest difference being overrepresentation of Lactobacillaceae at family taxonomic level. Correlation analyses highlighted multiple associations between clinical characteristics and select taxa, whilst constipation severity, physical activity and pharmacological therapies associated with changes in beta diversity. The random forest model of PD, incorporating taxonomic data at the genus level and carbohydrate contribution to total energy demonstrated the best predictive capacity [Area under the ROC Curve (AUC) of 0.74]. CONCLUSION: The notable differences in GM diversity and composition when combined with clinical measures and nutritional data enabled the development of a predictive model to identify PD. These findings support the combination of GM and nutritional data as a potentially useful biomarker of PD to improve diagnosis and guide clinical management.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8

Curated date: 2024/03/14

Curator: Assel

Revision editor(s): Assel, Peace Sandy

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 , Blood 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,Portion of blood,Vertebrate blood,Whole blood,Blood,blood

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: Participants with Parkinson's Disease

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with a clinical diagnosis of idiopathic PD according to the UK Parkinson’s Disease Society Brain Bank Diagnostic Criteria

Group 0 sample size Number of subjects in the control (unexposed) group: 81

Group 1 sample size Number of subjects in the case (exposed) group: 103

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): All participants did not receive antibiotics or probiotic supplements for at least 1-month prior to sample collection.

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: ANOVA

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index, sex

Alpha Diversity

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

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8

Curated date: 2024/03/15

Curator: Assel

Revision editor(s): Assel

Source: Table 3

Description: Gastrointestinal microbiota compositional differences between Parkinson’s Disease patients and Household Controls.

Abundance in Group 1: increased abundance in Participants with Parkinson's Disease

NCBI	Quality Control	Links
Bifidobacterium
Butyricimonas
Candidatus Soleaferrea sp.
Faecalibacterium sp. UBA1819
Flavonifractor
Ruminococcus sp.

Revision editor(s): Assel

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8

Curated date: 2024/03/15

Curator: Assel

Revision editor(s): Assel, Ayibatari

Source: Table 3

Description: Gastrointestinal microbiota compositional differences between Parkinson’s Disease patients and Household Controls.

Abundance in Group 1: decreased abundance in Participants with Parkinson's Disease

NCBI	Quality Control	Links
Agathobacter
Butyricicoccus
Erysipelotrichaceae bacterium
Fusicatenibacter
Lachnospiraceae bacterium ND3006
Ruminococcus gauvreauii
Eubacterium xylanophilum

Revision editor(s): Assel, Ayibatari