Alteration of the fecal microbiota in Chinese patients with Parkinson's disease

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/23

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29501802

DOI Digital object identifier for electronic documents.

10.1016/j.bbi.2018.02.016

URI

Authors

Qian Y, Yang X, Xu S, Wu C, Song Y, Qin N, Chen SD, Xiao Q

Journal

Brain, behavior, and immunity

Year

2018

Keywords:

16S rRNA gene, Gut microbiota, Neurodegenerative disorder

Emerging evidences suggest that gut microbiota dysbiosis plays a role in Parkinson's disease (PD). However, the alterations in fecal microbiome in Chinese PD patients remains unknown. This case-control study was conducted to explore fecal microbiota compositions in Chinese PD patients. Microbiota communities in the feces of 45 patients and their healthy spouses were investigated using high-throughput Illumina Miseq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene. The relationships between fecal microbiota and PD clinical characteristics were analyzed. The structure and richness of the fecal microbiota differed between PD patients and healthy controls. Genera Clostridium IV, Aquabacterium, Holdemania, Sphingomonas, Clostridium XVIII, Butyricicoccus and Anaerotruncus were enriched in the feces of PD patients after adjusting for age, gender, body mass index (BMI), and constipation. Furthermore, genera Escherichia/Shigella were negatively associated with disease duration. Genera Dorea and Phascolarctobacterium were negatively associated with levodopa equivalent doses (LED). Among the non-motor symptoms (NMSs), genera Butyricicoccus and Clostridium XlVb were associated with cognitive impairment. Overall, we confirmed that gut microbiota dysbiosis occurs in Chinese patients with PD. A well-controlled population involved was beneficial for the identification of microbiota associated with diseases. Additionally, the fecal microbiota was closely related to PD clinical characteristics. Elucidating these differences in the fecal microbiome will provide a foundation to improve our understanding the pathogenesis of PD and to support the potentially therapeutic options modifying the gut microbiota.

Experiment 1

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Curated date: 2022/01/15

Curator: Fcuevas3

Revision editor(s): WikiWorks, Claregrieve1, Fcuevas3, Peace Sandy, Miss Lulu

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

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: All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.

Group 0 sample size Number of subjects in the control (unexposed) group: 45

Group 1 sample size Number of subjects in the case (exposed) group: 45

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: 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

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

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

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/23

Curated date: 2022/01/15

Curator: Fcuevas3

Revision editor(s): Claregrieve1, Fcuevas3, WikiWorks

Source: Figure 3A.

Description: Taxonomic differences of fecal microbiota in PD and healthy groups

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

NCBI	Quality Control	Links
Acinetobacter
Alistipes
Aquabacterium
Butyricicoccus
Chitinophagaceae
Clostridium
Desulfovibrio
Erysipelotrichaceae
Erysipelotrichia
Bacillota
Klebsiella
Moraxellaceae
Nitrososphaeraceae
Paraprevotella
Rhizobiaceae
Rikenellaceae
Sphingobacteriales
Sphingobacteriia
Sphingomonadaceae
Sphingomonadales
Sphingomonas
Nitrososphaerota
Lysobacteraceae
Lysobacterales
unclassified Desulfovibrio
Burkholderiales genera incertae sedis
Nitrososphaerales
Nitrososphaera
Lachnospiraceae incertae sedis
Pseudomonadales