Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- United States of America
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parkinson disease, mitochondrial Parkinson disease, mitochondrial,parkinson disease, mitochondrial
- 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 (PD patients)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 220
- Group 1 sample size Number of subjects in the case (exposed) group
- 438
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- WMS
- 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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
Signature 1
Needs review
Source: Figure 6b, Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using ANCOM statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Signature 2
Needs review
Source: Figure 6b, Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using ANCOM statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
