The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies/Experiment 8

From BugSigDB


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Subjects

Location of subjects
Australia
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
Blood , Feces Portion of blood,Vertebrate blood,Whole blood,Blood,blood,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
Pre DAT(device assisted therapy)
Group 1 name Corresponds to the case (exposed) group for case-control studies
DBS(deep brain stimulation)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of DBS therapy on parkinson's disease patients at 12 month
Group 0 sample size Number of subjects in the control (unexposed) group
74
Group 1 sample size Number of subjects in the case (exposed) group
9
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 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).
centered log-ratio
Statistical test
ANOVA
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)?
Yes
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, diet, sex, constipation

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: DBS therapy patients showed overrepresentation of these taxa (t=12moths)

Abundance in Group 1: increased abundance in DBS(deep brain stimulation)

NCBI Quality ControlLinks
Bacillaceae
Bacillus
Citrobacter
Faecalicoccus
Methanobacteriaceae
Methanobrevibacter
Morganella
Prevotella
Spirochaetaceae
Treponema
Veillonella

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: DBS therapy patients showed uderrepresentation of these taxa after 12 months initiation

Abundance in Group 1: decreased abundance in DBS(deep brain stimulation)

NCBI Quality ControlLinks
Acetanaerobacterium
Anaerotruncus
Flavonifractor
Hespellia
Howardella

Revision editor(s): Bolanle