Alteration of the fecal microbiota in Chinese patients with Parkinson's disease/Experiment 1

From BugSigDB


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

Curated date: 2022/01/15

Curator: Fcuevas3

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

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
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)
Participants taking antibiotics or probiotic supplements within the three months 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
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

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

Curated date: 2022/01/15

Curator: Fcuevas3

Revision editor(s): Claregrieve1, Fcuevas3

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 ControlLinks
Acinetobacter
Alistipes
Aquabacterium
Butyricicoccus
Chitinophagaceae
Clostridium
Desulfovibrio
Erysipelotrichaceae
Erysipelotrichia
Bacillota
Klebsiella
Moraxellaceae
Nitrososphaeraceae
Paraprevotella
Rhizobiaceae
Rikenellaceae
Sphingobacteriales
Sphingobacteriia
Sphingomonadaceae
Sphingomonadales
Sphingomonas
Nitrososphaerota
Xanthomonadaceae
Xanthomonadales
unclassified Desulfovibrio
Burkholderiales genera incertae sedis
Nitrososphaerales
Nitrososphaera
Lachnospiraceae incertae sedis
Pseudomonadales

Revision editor(s): Claregrieve1, Fcuevas3

Signature 2

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

Curated date: 2022/01/22

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Figure 3A.

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

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

NCBI Quality ControlLinks
Actinomycetales
Lactobacillaceae
Lactobacillus
Flavobacteriales
Flavobacteriia
Sediminibacterium

Revision editor(s): Fcuevas3