Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study/Experiment 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tobacco smoke exposure measurement Tobacco smoke exposure measurement,tobacco smoke exposure 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 cigarette smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who reported smoking more than 100 cigarettes in their lifetime, smoking a cigarette in the last 5 days, and not using any alternative tobacco product in the last 5 days (the 90 with highest measured serum cotinine were selected)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 86
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
- Statistical test
- edgeR
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, diabetes mellitus, physical activity, education level, race, sex, Confounders controlled for: "self-reported gum disease" 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.self-reported gum disease
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Supplementary Fig. 4 , Supplementary Fig. 5
Description: Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers.
Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).
Abundance in Group 1: decreased abundance in Current cigarette smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Bergeyella | ||
| Bifidobacterium | ||
| Cardiobacterium | ||
| Gemella | ||
| Haemophilus | ||
| Lachnoanaerobaculum | ||
| Lactococcus | ||
| Lautropia | ||
| Neisseria | ||
| Porphyromonas | ||
| Streptococcus | ||
| Pseudomonadota |
Revision editor(s): Atrayees, Peace Sandy
Signature 2
Source: Supplementary Fig. 4 , Supplementary Fig. 5
Description: Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers.
Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).
Abundance in Group 1: increased abundance in Current cigarette smokers
Revision editor(s): Atrayees, Peace Sandy
