Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-3-20
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zapała B, Stefura T, Wójcik-Pędziwiatr M, Kabut R, Bałajewicz-Nowak M, Milewicz T, Dudek A, Stój A, Rudzińska-Bar M
Journal
Journal of clinical medicine
Year
2021
Keywords:
Parkinson’s disease, gut microbiome, microbiota
Gut microbiome and colonic inflammation can be associated with the predisposition and progression of Parkinson's disease (PD). The presented study aimed to compare gastrointestinal microbiota composition between patients diagnosed with PD and treated only with Levodopa to healthy controls. In this prospective study, patients were recruited in 1 academic hospital from July 2019 to July 2020. The detailed demographic data and medical history were collected using a set of questionnaires. Fecal samples were obtained from all participants. Next-Generation Sequencing was used to assess the microbiota composition. The endpoint was the difference in composition of the gut microbiota. In this study, we enrolled 27 hospitalized PD patients with well-controlled symptoms. The control group included 44 healthy subjects matched for age. Among PD patients, our results presented a higher abundance of Bacteroides phylum, class Corynebacteria among phylum Actinobacteria, class Deltaproteobacteria among phylum Proteobacteria, and genera such as Butyricimonas, Robinsoniella, and Flavonifractor. The species Akkermansia muciniphila, Eubacterium biforme, and Parabacteroides merdae were identified as more common in the gut microbiota of PD patients. In conclusion, the patients diagnosed with PD have significantly different gut microbiota profiles in comparison with healthy controls.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-3-20

Curated date: 2024/03/07

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu, Peace Sandy

Subjects

Location of subjects
Poland
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
Hospitalized Patients diagnosed with Parkinson's disease with well-controlled symptoms.
Group 0 sample size Number of subjects in the control (unexposed) group
44
Group 1 sample size Number of subjects in the case (exposed) group
27
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 weeks

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, MGISEQ-2000

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
Matched on Factors on which subjects have been matched on in a case-control study
age

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
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-20

Curated date: 2024/03/07

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu, Peace Sandy

Source: Figure 6 , Figure 7

Description: Bacterial species are more abundant in the PD than in the control group, according to the LefSE analysis.

Cladogram generated by LEfSe shows the taxa differences between PD patients (2) and healthy controls (1).

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

NCBI Quality ControlLinks
Acidaminobacter hydrogenoformans
Akkermansia muciniphila
Bacteroides caccae
Bilophila wadsworthia
Christensenella timonensis
Coriobacteriia
Deltaproteobacteria
Erysipelotrichia
Flavobacteriia
Flavonifractor plautii
Gammaproteobacteria
Holdemanella biformis
Hungatella hathewayi
Parabacteroides distasonis
Parabacteroides merdae
Phocaeicola massiliensis
Clostridium thermosuccinogenes
Pseudomonadota
Robinsoniella peoriensis
Ruminococcus gauvreauii
Streptococcus mutans
Synergistota
Verrucomicrobiae
Verrucomicrobiota
[Clostridium] viride
[Ruminococcus] torques

Revision editor(s): Adenike Oladimeji-Kasumu, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-20

Curated date: 2024/03/08

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu, Peace Sandy

Source: Figure 6 , Figure 7

Description: Bacterial species are more abundant in the PD than in the control group, according to the LefSE analysis.

Cladogram generated by LEfSe shows the taxa differences between PD patients (2) and healthy controls (1).

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

NCBI Quality ControlLinks
Anaerobutyricum hallii
Anaerostipes butyraticus
Bifidobacterium longum
Blautia faecis
Blautia obeum
Enterococcus faecalis
Eubacterium ramulus
Faecalibacterium prausnitzii
Intestinibacillus massiliensis
Lachnospira eligens
Megamonas funiformis
Ruminococcus albus
Clostridia
Bacillota
Fusobacteriia

Revision editor(s): Adenike Oladimeji-Kasumu, Peace Sandy