Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-23
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Antonello G, Blostein F, Bhaumik D, Davis E, Gögele M, Melotti R, Pramstaller P, Pattaro C, Segata N, Foxman B, Fuchsberger C
Journal
Scientific reports
Year
2023
The oral microbiota plays an important role in the exogenous nitrate reduction pathway and is associated with heart and periodontal disease and cigarette smoking. We describe smoking-related changes in oral microbiota composition and resulting potential metabolic pathway changes that may explain smoking-related changes in disease risk. We analyzed health information and salivary microbiota composition among 1601 Cooperative Health Research in South Tyrol participants collected 2017-2018. Salivary microbiota taxa were assigned from amplicon sequences of the 16S-V4 rRNA and used to describe microbiota composition and predict metabolic pathways. Aerobic taxa relative abundance decreased with daily smoking intensity and increased with years since cessation, as did inferred nitrate reduction. Former smokers tended to be more similar to Never smokers than to Current smokers, especially those who had quit for longer than 5 years. Cigarette smoking has a consistent, generalizable association on oral microbiota composition and predicted metabolic pathways, some of which associate in a dose-dependent fashion. Smokers who quit for longer than 5 years tend to have salivary microbiota profiles comparable to never smokers.

Experiment 1


Reviewed Marked as Reviewed by Folakunmi on 2024-2-23

Curated date: 2023/11/05

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Subjects

Location of subjects
Italy
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
Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.
Group 0 sample size Number of subjects in the control (unexposed) group
880
Group 1 sample size Number of subjects in the case (exposed) group
326
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
12 weeks

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).
raw counts
Statistical test
DESeq2
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, number of teeth measurement, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-22

Curated date: 2023/11/07

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: figure 1

Description: Heatmap of the 44 genera diferentially abundant between Current and Never smokers

Abundance in Group 1: increased abundance in Current smokers

NCBI Quality ControlLinks
Actinomyces
Alloscardovia
Atopobium
Bacteroidia
Bifidobacterium
Bulleidia
Cryptobacterium
Dialister
Filifactor
Fretibacterium
Lactobacillus
Megasphaera
Mitsuokella
Mycoplasma
Rothia
Stomatobaculum
Treponema
Veillonella
uncultured Peptostreptococcus sp.

Revision editor(s): OdigiriGreat, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-22

Curated date: 2023/11/07

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: figure 1

Description: Result of the Heatmap of the 44 genera diferentially abundant between Current and Never smokers.

Abundance in Group 1: decreased abundance in Current smokers

NCBI Quality ControlLinks
Abiotrophia
Aggregatibacter
Alloprevotella
Bergeyella
Candidatus Absconditabacteria
Capnocytophaga
Cardiobacterium
Catonella
Fusobacterium
Haemophilus
Kingella
Lautropia
Leptotrichia
Neisseria
Ottowia
Peptococcus
Peptostreptococcus
Porphyromonas
uncultured Lachnospiraceae bacterium
uncultured Peptostreptococcus sp.
Ruminococcaceae_G-1Ruminococcaceae_G-1
Candidatus Gracilibacteria

Revision editor(s): OdigiriGreat, Folakunmi

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-2-23

Curated date: 2024/02/23

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals who quit smoking 17.96 years on average
Group 1 sample size Number of subjects in the case (exposed) group
395

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
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged