Cigarette smoking and oral microbiota in low-income and African-American populations/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-1
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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking status measurement Smoking status measurement,smoking status measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Never-Smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Current-Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 547
- Group 1 sample size Number of subjects in the case (exposed) group
- 592
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Participants who took antibiotics within a year before sample collection.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Logistic Regression
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol drinking, body mass index, race, sex, Matched on: "total energy intake" 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.total energy intake, Matched on: "disease status at the first follow-up and sequencing batch" 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.disease status at the first follow-up and sequencing batch, oral hygiene
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-1
Curated date: 2023/03/14
Curator: Nnadichioma
Revision editor(s): Merit, Atrayees, Nnadichioma, Aiyshaaaa
Source: Table 2,3,and 4
Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers
Abundance in Group 1: increased abundance in Current-Smokers
Revision editor(s): Merit, Atrayees, Nnadichioma, Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-1
Source: Table 3 and 4
Description: Individual taxa showing a differential relative abundance between current-smokers and never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers
Abundance in Group 1: decreased abundance in Current-Smokers
Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees
