Analysis of the Gut Microflora in Patients With Parkinson's Disease

Study information

Reviewed Marked as Reviewed by Lwaldron on 2022/07/1

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31824239

DOI Digital object identifier for electronic documents.

10.3389/fnins.2019.01184

URI

Authors

Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B, Alkasir R

Journal

Frontiers in neuroscience

Year

2019

Keywords:

16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora

This study was conducted to explore the composition of the fecal microflora of Chinese Parkinson's disease (PD) patients, as well as to explore links between PD clinical features and antiparkinsonian medications on the gut microflora. Seventy-two PD cases [59 patients suffering from PD for >1 year (OPD) and 13 new PD (NPD) patients] were studied. Microflora communities in the feces of the patients and corresponding healthy controls (HCs) were examined using high-throughput Illumina MiSeq sequencing targeting the 16S rRNA gene. The gut microflora of OPD patients contained high levels of Rikenellaceae compared to corresponding HCs. In addition, significantly higher levels of Turicibacteraceae were found in the NPD group compared to the corresponding HCs. The genera Turicibacter and Prevotella were significantly correlated with the PD severity scores. Our findings that some fecal microflora were closely related to PD clinical characteristics may enhance our understanding of the pathogenesis and treatment of PD.

Experiment 1

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Reviewed Marked as Reviewed by Rimsha on 2022/03/2

Curated date: 2021/11/29

Curator: Fcuevas3

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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 without any form of Parkinson's Disease

Group 1 name Corresponds to the case (exposed) group for case-control studies: NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.

Group 0 sample size Number of subjects in the control (unexposed) group: 68

Group 1 sample size Number of subjects in the case (exposed) group: 13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): The use of any antibiotics or probiotics within 90 days before collection of the samples.

Lab analysis

Sequencing type: 16S

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: Illumina

Statistical Analysis

Statistical test: Metastats

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

Matched on Factors on which subjects have been matched on in a case-control study: age, life style

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Signature 1

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Source: Figure 3. Genus level comparison among NPD samples.

Description: Genus-level comparison among NPD samples collected at different times.

Abundance in Group 1: increased abundance in NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.

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Turicibacter

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Source: FIGURE 3

Description: Genus-level comparison among NPD samples collected at different times.

Abundance in Group 1: decreased abundance in NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.

NCBI	Quality Control	Links
Paraprevotella
Ruminococcus
Streptococcus

Revision editor(s): Rimsha, Fcuevas3, WikiWorks

Experiment 2

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Curated date: 2021/11/29

Curator: Fcuevas3

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Group 1 name Corresponds to the case (exposed) group for case-control studies: NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 5 days after treatment.

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.01

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Signature 1

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Curated date: 2021/11/29

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Source: FIGURE 3.

Description: Genus-level comparison among NPD samples collected at different times.

Abundance in Group 1: increased abundance in NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.

NCBI	Quality Control	Links
Turicibacter

Revision editor(s): Rimsha, Fcuevas3, WikiWorks

Experiment 3

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.