Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease/Experiment 3
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, smoking status, Confounders controlled for: "dessert consumption frequency" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.dessert consumption frequency, Confounders controlled for: "flossing teeth frequency" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.flossing teeth frequency, Confounders controlled for: "laxative use in the past month" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.laxative use in the past month, Confounders controlled for: "number of weekly bowel movements" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.number of weekly bowel movements, Confounders controlled for: "US census region" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.US census region
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Data 2
Description: Significantly differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) identified using the ANCOM statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Signature 2
Needs review
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases (after adjustment for covariates) using ANCOM statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
