Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE, Waldron L
Journal
Annals of epidemiology
Year
2019
Keywords:
16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco
PURPOSE: The effect of tobacco exposure on the oral microbiome has not been established. METHODS: We performed amplicon sequencing of the 16S ribosomal RNA gene V4 variable region to estimate bacterial community characteristics in 259 oral rinse samples, selected based on self-reported smoking and serum cotinine levels, from the 2013-2014 New York City Health and Nutrition Examination Study. We identified differentially abundant operational taxonomic units (OTUs) by primary and secondhand tobacco exposure, and used "microbe set enrichment analysis" to assess shifts in microbial oxygen utilization. RESULTS: Cigarette smoking was associated with depletion of aerobic OTUs (Enrichment Score test statistic ES = -0.75, P = .002) with a minority (29%) of aerobic OTUs enriched in current smokers compared with never smokers. Consistent shifts in the microbiota were observed for current cigarette smokers as for nonsmokers with secondhand exposure as measured by serum cotinine levels. Differential abundance findings were similar in crude and adjusted analyses. CONCLUSIONS: Results support a plausible link between tobacco exposure and shifts in the oral microbiome at the population level through three lines of evidence: (1) a shift in microbiota oxygen utilization associated with primary tobacco smoke exposure; (2) consistency of abundance fold changes associated with current smoking and shifts along the gradient of secondhand smoke exposure among nonsmokers; and (3) consistency after adjusting for a priori hypothesized confounders.
Experiment 1
Reviewed Marked as Reviewed by Lwaldron on 2024-1-9
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
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-9
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
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-9
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
Experiment 2
Reviewed Marked as Reviewed by Lwaldron on 2024-1-9
Differences from previous experiment shown
Subjects
- 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
- Alternative Tobacco Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who used e-cigarettes, hookah, and/or cigar or cigarillo but not cigarettes
- Group 1 sample size Number of subjects in the case (exposed) group
- 49
Lab analysis
Statistical Analysis
- 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
Reviewed Marked as Reviewed by Lwaldron on 2024-1-9
Source: Text
Description: Differential abundance of OTUs from participants who used e-cigarettes, hookah, and/or cigar or cigarillo but not cigarettes
Abundance in Group 1: increased abundance in Alternative Tobacco Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Pseudomonadota |
Revision editor(s): Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2024-1-9
Source: Text
Description: Differential abundance of OTUs from participants who used e-cigarettes, hookah, and/or cigar/cigarillo but not cigarettes
Abundance in Group 1: decreased abundance in Alternative Tobacco Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| uncultured bacterium |
Revision editor(s): Peace Sandy
Experiment 3
Reviewed Marked as Reviewed by Lwaldron on 2024-1-9
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- participants who only smoked hookah
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- participants who only smoked hookah
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
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
Reviewed Marked as Reviewed by Lwaldron on 2024-1-9
Source: Text
Description: In those who only smoked hookah (n = 28), genera Porphyromonas, Leptotrichia, Streptobacillus, Fusobacterium, and an uncultured bacterium from Saccharibacteria were depleted.
Abundance in Group 1: decreased abundance in participants who only smoked hookah
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas | ||
| Leptotrichia | ||
| Streptobacillus | ||
| Fusobacterium | ||
| uncultured bacterium |
Revision editor(s): Peace Sandy
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