Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study

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Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


Needs review

Curated date: 2023/03/28

Curator: Atrayees

Revision editor(s): Atrayees

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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
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

Signature 1

Needs review

Curated date: 2023/03/28

Curator: Atrayees

Revision editor(s): Atrayees

Source: Supplementary Fig. 4

Description: Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers.

Abundance in Group 1: decreased abundance in Current cigarette smokers

NCBI Quality ControlLinks
Actinobacillus
Bergeyella
Bifidobacterium
Gemella
Lachnoanaerobaculum
Lactococcus
Lautropia
Porphyromonas
Streptococcus
Neisseria
Cardiobacterium
Haemophilus

Revision editor(s): Atrayees

Signature 2

Needs review

Curated date: 2023/03/28

Curator: Atrayees

Revision editor(s): Atrayees, Peace Sandy

Source: Supplementary Fig. 4

Description: Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers.

Abundance in Group 1: increased abundance in Current cigarette smokers

NCBI Quality ControlLinks
Alloprevotella
Anaeroglobus
Campylobacter
Fretibacterium
Lactobacillus
Leptotrichia
Megasphaera
Prevotella
Pseudomonas
Rothia
Treponema
Veillonella
Muribaculaceae

Revision editor(s): Atrayees, Peace Sandy

Signature 3

Needs review

Curated date: 2023/03/28

Curator: Atrayees

Revision editor(s): Atrayees

Source: Supplementary Fig. 5

Description: 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 ControlLinks
Pseudomonadota

Revision editor(s): Atrayees

Signature 4

Needs review

Curated date: 2023/03/28

Curator: Atrayees

Revision editor(s): Atrayees

Source: Supplementary Fig. 5

Description: 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

NCBI Quality ControlLinks
Synergistota
Actinomycetota
Candidatus Saccharibacteria
Spirochaetota

Revision editor(s): Atrayees