Alteration of the fecal microbiota in North-Eastern Han Chinese population with sporadic Parkinson's disease

Study information

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31200089

DOI Digital object identifier for electronic documents.

10.1016/j.neulet.2019.134297

URI

https://pubmed.ncbi.nlm.nih.gov/31200089/

Authors

Li F, Wang P, Chen Z, Sui X, Xie X, Zhang J

Journal

Neuroscience letters

Year

2019

Keywords:

16S rRNA gene, Gut microbiome, Microbiota–gut–brain axis, Parkinson’s disease, Pathogenesis

Studies have confirmed that the gut microbiota may be involved in the pathogenesis of Parkinson's disease(PD). However, the alterations in fecal microbiome in North-eastern Han sporadic PD patients remains unknown. This case control study was conducted to explore fecal microbiota compositions in North-eastern Han sporadic PD patients. The gut microbiota composition of 10 patients with sporadic PD and over 65 age and 10 matched controls was analyzed in this study. Microbiota communities in the feces were investigated using high-throughput Illumina Miseq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene. The structure and richness of the fecal microbiota differed between PD patients and healthy controls. We had observed that the overall composition of gut microbiota in North-eastern Han Chinese healthy and PD patients was slightly different. The abundance of the family of Bacteroides and Prevotellaceae were significantly increased in heathy controls while the abundance of Ruminococcaceae, Verrucomicrobiaceae, Porphyromondaceae, Hydrogenoanaerobacterium and Lachnospiraceae NK4A were significantly enriched in North-eastern Han Chinese patients with PD. Sporadic PD patients North-eastern Han China is accompanied by alterations in the abundance of specific gut microbes. Our findings will provide a foundation to improve our understanding the pathogenesis of PD.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2023/05/03

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin

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 Controls

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: Patients with sporadic PD and over 65 age.

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): One month.

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): .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

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2023/05/04

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin, Chloe

Source: Figure 5

Description: The histogram of the LDA scores presents species whose abundance showed significant differences between the heathy controls and PD patients in the fecal samples. The length of each bin, namely, the LDA score. A p-value of < 0.05 and a score ≥ 2.0 were considered significant in KW rank sum test and Wilcox tests, respectively. The horizontal straight line in the panel indicated the group means, and the dotted line indicated the group medians.

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

NCBI	Quality Control	Links
Bacteria
Akkermansia
Butyricimonas
Eisenbergiella
Eubacterium ventriosum
Holdemania
Hydrogenoanaerobacterium
Intestinimonas
Lachnospiraceae
Odoribacter
Oscillospiraceae
Parasutterella
Porphyromonadaceae
Subdoligranulum
Verrucomicrobiaceae
Verrucomicrobiae
Verrucomicrobiales
Verrucomicrobiota

Revision editor(s): Jacquelynshevin, Chloe

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2023/05/04

Curator: Jacquelynshevin

Revision editor(s): Jacquelynshevin, Chloe, WikiWorks

Source: Figure 5

Description: The histogram of the LDA scores presents species whose abundance showed significant differences between the heathy controls and PD patients in the fecal samples. The length of each bin, namely, the LDA score. A p-value of < 0.05 and a score ≥ 2.0 were considered significant in KW rank sum test and Wilcox tests, respectively. The horizontal straight line in the panel indicated the group means, and the dotted line indicated the group medians.

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

NCBI	Quality Control	Links
Bacteria
Allisonella
Bacteroidales
Bacteroides
Clostridiaceae
Clostridium
Collinsella
Holdemanella
Lactobacillaceae
Prevotellaceae
Tyzzerella

Revision editor(s): Jacquelynshevin, Chloe, WikiWorks