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

From BugSigDB
Needs review
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


Needs review

Curated date: 2023/11/05

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
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).
relative abundances
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

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

Needs review

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

Needs review

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


Needs review

Curated date: 2023/11/12

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former smokers (0-1 year)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Former smokers who quit smoking 0-1 year prior to study
Group 0 sample size Number of subjects in the control (unexposed) group
656
Group 1 sample size Number of subjects in the case (exposed) group
21

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

Signature 1

Needs review

Curated date: 2023/11/12

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: increased abundance in Former smokers (0-1 year)

NCBI Quality ControlLinks
Abiotrophia
Aggregatibacter
Bulleidia
Cryptobacterium
Dialister
Fretibacterium
Kingella
Mycoplasma
uncultured Peptostreptococcus sp.

Revision editor(s): OdigiriGreat, Folakunmi

Signature 2

Needs review

Curated date: 2023/11/12

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: decreased abundance in Former smokers (0-1 year)

NCBI Quality ControlLinks
Alloscardovia
Candidatus Absconditabacteria
Capnocytophaga
Catonella
Haemophilus
Lachnospiraceae
Lautropia
Neisseria
Ottowia
Peptococcus
Peptostreptococcus
Stomatobaculum
uncultured Peptostreptococcus sp.

Revision editor(s): OdigiriGreat, Folakunmi

Experiment 3


Needs review

Curated date: 2023/11/12

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former smokers (2-3 year)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Former smokers who quit smoking 2-3 year prior to study
Group 1 sample size Number of subjects in the case (exposed) group
30

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

Signature 1

Needs review

Curated date: 2023/11/13

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: increased abundance in Former smokers (2-3 year)

NCBI Quality ControlLinks
Bergeyella
Cardiobacterium
Haemophilus

Revision editor(s): OdigiriGreat

Signature 2

Needs review

Curated date: 2023/11/13

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: decreased abundance in Former smokers (2-3 year)

NCBI Quality ControlLinks
Actinomyces
Aggregatibacter
Alloscardovia
Bifidobacterium
Bulleidia
Candidatus Absconditabacteria
Cryptobacterium
Dialister
Filifactor
Fretibacterium
Lactobacillus
Leptotrichia
Mitsuokella
Mycoplasma
Neisseria
Ottowia
Porphyromonas
Rothia
Stomatobaculum
Veillonella
uncultured Peptostreptococcus sp.
Lachnospiraceae G_3Lachnospiraceae G_3
Ruminococcaceae G_1Ruminococcaceae G_1
Candidatus Gracilibacteria

Revision editor(s): OdigiriGreat, Folakunmi

Experiment 4


Needs review

Curated date: 2023/11/15

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former smokers (4-5 year)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Former smokers who quit smoking 4-5year prior to study
Group 1 sample size Number of subjects in the case (exposed) group
25

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

Signature 1

Needs review

Curated date: 2023/11/15

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: increased abundance in Former smokers (4-5 year)

NCBI Quality ControlLinks
Actinomyces
Atopobium
Bifidobacterium
Catonella
Leptotrichia
Megasphaera
Mitsuokella
Veillonella
uncultured Peptostreptococcus sp.
Bacteroides sp.

Revision editor(s): OdigiriGreat, Folakunmi

Signature 2

Needs review

Curated date: 2023/11/15

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: decreased abundance in Former smokers (4-5 year)

NCBI Quality ControlLinks
Abiotrophia
Aggregatibacter
Bergeyella
Candidatus Gracilibacteria
Capnocytophaga
Cardiobacterium
Fusobacterium
Kingella
Lautropia
Neisseria
Porphyromonas
uncultured Peptostreptococcus sp.

Revision editor(s): OdigiriGreat, Folakunmi

Experiment 5


Needs review

Curated date: 2023/11/16

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former smokers (5-10 years)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Former smokers who quit smoking 5-10 years prior to study
Group 1 sample size Number of subjects in the case (exposed) group
35

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

Signature 1

Needs review

Curated date: 2023/11/16

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: increased abundance in Former smokers (5-10 years)

NCBI Quality ControlLinks
Candidatus Absconditabacteria
Ottowia
Lautropia
Candidatus Gracilibacteria
Peptostreptococcus
Lactobacillus
Alloscardovia
Stomatobaculum
Filifactor
Treponema
Mycoplasma

Revision editor(s): OdigiriGreat

Signature 2

Needs review

Curated date: 2023/11/16

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: decreased abundance in Former smokers (5-10 years)

NCBI Quality ControlLinks
Cryptobacterium
Dialister
Ruminococcaceae_G1Ruminococcaceae_G1
Peptococcus
Alloprevotella
Leptotrichia
Mitsuokella
Bergeyella
Fusobacterium
Abiotrophia
Aggregatibacter
Bacteroides sp.
Lachnospiraceae_G3Lachnospiraceae_G3
Capnocytophaga

Revision editor(s): OdigiriGreat

Experiment 6


Needs review

Curated date: 2023/11/16

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former smokers (11-62 year)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Former smokers who quit smoking 11-62 years prior to study
Group 1 sample size Number of subjects in the case (exposed) group
145

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

Signature 1

Needs review

Curated date: 2023/11/16

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: increased abundance in Former smokers (11-62 year)

NCBI Quality ControlLinks
Porphyromonas
Capnocytophaga
Neisseria

Revision editor(s): OdigiriGreat

Signature 2

Needs review

Curated date: 2023/11/16

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 3

Description: The salivary microbiota of individuals who quit smoking (n=369) showed multiple-year perturbation and tends to resemble Never smokers’ profles within 5 years. (A) Heatmap of the relationship between the years since quitting smoking and the mean relative abundance of genera previously found signifcantly associated with smoking

Abundance in Group 1: decreased abundance in Former smokers (11-62 year)

NCBI Quality ControlLinks
Cryptobacterium
Dialister
Megasphaera
Treponema
Fretibacterium
uncultured Peptostreptococcus sp.
Kingella
Peptostreptococcus
Atopobium
Bacteroides sp.
Bifidobacterium
Veillonella
Cardiobacterium
Haemophilus

Revision editor(s): OdigiriGreat