Cigarette smoking and oral microbiota in low-income and African-American populations

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Yang Y, Zheng W, Cai QY, Shrubsole MJ, Pei Z, Brucker R, Steinwandel MD, Bordenstein SR, Li Z, Blot WJ, Shu XO, Long J
Journal
Journal of epidemiology and community health
Year
2019
BACKGROUND: Cigarette smoking is a common risk factor for diseases and cancers. Oral microbiota is also associated with diseases and cancers. However, little is known about the impact of cigarette smoking on the oral microbiota, especially among ethnic minority populations. METHODS: We investigated cigarette smoking in relationship with the oral microbiota in a large population of predominately low-income and African-American participants. Mouth rinse samples were collected from 1616 participants within the Southern Community Cohort Study, including 592 current-smokers, 477 former-smokers and 547 never-smokers. Oral microbiota was profiled by 16S ribosomal RNA gene deep sequencing. RESULTS: Current-smokers showed a different overall microbial composition from former-smokers (p=6.62×10-7) and never-smokers (p=6.00×10-8). The two probiotic genera, Bifidobacterium and Lactobacillus, were enriched among current-smokers when compared with never-smokers, with Bonferroni-corrected p values (PBonferroni ) of 1.28×10-4 and 5.89×10-7, respectively. The phylum Actinobacteria was also enriched in current-smokers when compared with never-smokers, with a median relative abundance of 12.35% versus 9.36%, respectively, and with a PBonferroni =9.11×10-11. In contrast, the phylum Proteobacteria was depleted in current smokers (PBonferroni =5.57×10-13), with the relative abundance being almost three times that of never-smokers (7.22%) when compared with that of current-smokers (2.47%). Multiple taxa within these two phyla showed differences in abundance/prevalence between current-smokers and never-smokers at PBonferroni <0.05. The differences in the overall microbial composition and abundance/prevalence of most taxa were observed among both African-Americans and European-Americans. Meanwhile, such differences were not observed between former-smokers and never-smokers. CONCLUSION: Smoking has strong impacts on oral microbial community, which was recovered after smoking cessation.

Experiment 1


Needs review

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.
Group 0 sample size Number of subjects in the control (unexposed) group
547
Group 1 sample size Number of subjects in the case (exposed) group
592
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants who took antibiotics within a year before sample collection.

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
Logistic Regression
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)?
No
Matched on Factors on which subjects have been matched on in a case-control study
age, body mass index, race, sex, Matched on: "alcohol consumption" 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.alcohol consumption, Matched on: "total energy intake" 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.total energy intake, Matched on: "disease status at the first follow-up and sequencing batch" 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.disease status at the first follow-up and sequencing batch, Matched on: "oral health status" 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.oral health status


Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Needs review

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Atrayees

Source: Table 2,3,and 4

Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Current-Smokers

NCBI Links
Actinomyces graevenitzii
Actinomyces lingnae
Bifidobacterium longum
Lactobacillus crispatus
Lactobacillus gasseri
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Megasphaera micronuciformis
Prevotella sp. oral taxon 313
Rothia mucilaginosa
Streptococcus sp. oral taxon 057
Treponema denticola
Kingella elongataKingella elongata

Revision editor(s): Nnadichioma, Atrayees

Signature 2

Needs review

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa

Source: Table 3 and 4

Description: Individual taxa showing a differential relative abundance between current-smokers and never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers

Abundance in Group 1: decreased abundance in Current-Smokers

NCBI Links
Aggregatibacter
Capnocytophaga sputigena
Cardiobacterium
Enterococcus
Gemella
Haemophilus parahaemolyticus
Haemophilus paraphrohaemolyticus
Hoylesella nanceiensis
Kingella denitrificans
Lachnoanaerobaculum umeaense
Lachnospiraceae
Lautropia
Neisseria oralis
Neisseria pharyngis
Neisseria pharyngis subsp. flava
Streptococcus sp. oral taxon 070
[Eubacterium] infirmum
Streptococcus cristatus

Revision editor(s): Nnadichioma, Aiyshaaaa

Experiment 2


Needs review

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Former-Smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.
Group 0 sample size Number of subjects in the control (unexposed) group
547
Group 1 sample size Number of subjects in the case (exposed) group
477
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants who took antibiotics within a year before sample collection.

Lab analysis

Sequencing type
16S
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
Logistic Regression
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)?
No
Matched on Factors on which subjects have been matched on in a case-control study
age, body mass index, race, sex, Matched on: "alcohol consumption" 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.alcohol consumption, Matched on: "total energy intake" 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.total energy intake, Matched on: "oral health status" 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.oral health status, Matched on: "disease status at the first follow-up and sequencing batch" 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.disease status at the first follow-up and sequencing batch


Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Needs review

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa

Source: Table 2,3,and 4

Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Former-Smokers

NCBI Links
Actinomyces graevenitzii
Bifidobacterium longum
Haemophilus parahaemolyticus
Lachnoanaerobaculum umeaense
Lactobacillus crispatus
Lactobacillus gasseri
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Rothia mucilaginosa
Streptococcus cristatus
Streptococcus sp. oral taxon 057
K. elongataK. elongata
Actinomyces lingnae

Revision editor(s): Nnadichioma, Aiyshaaaa

Signature 2

Needs review

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa

Source: Table 3 and 4

Description: Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: decreased abundance in Former-Smokers

NCBI Links
Actinomyces
Aggregatibacter
Capnocytophaga sputigena
Cardiobacterium
Enterococcus
Gemella
Haemophilus paraphrohaemolyticus
Kingella denitrificans
Lachnoanaerobaculum umeaense
Lachnospiraceae
Lautropia
Megasphaera micronuciformis
Neisseria oralis
Neisseria pharyngis
Neisseria subflava
Prevotella nanceiensis DSM 19126 = JCM 15639
Prevotella sp. oral taxon 313
Streptococcus sp. oral taxon 070
Treponema denticola
[Eubacterium] infirmum
Lancefieldella parvula

Revision editor(s): Nnadichioma, Aiyshaaaa

Experiment 3


Needs review

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Former-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
Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.
Group 0 sample size Number of subjects in the control (unexposed) group
477
Group 1 sample size Number of subjects in the case (exposed) group
592
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants who took antibiotics within a year before sample collection.

Lab analysis

Sequencing type
16S
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
Logistic Regression
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)?
No
Matched on Factors on which subjects have been matched on in a case-control study
age, sex, race, body mass index, Matched on: "alcohol consumption" 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.alcohol consumption, Matched on: "total energy intake" 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.total energy intake, Matched on: "oral health status" 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.oral health status, Matched on: "disease status at the first follow-up and sequencing batch" 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.disease status at the first follow-up and sequencing batch


Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Needs review

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa

Source: Table 2, 3, and 4

Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Current-Smokers

NCBI Links
Actinomyces
Actinomyces graevenitzii
Actinomyces lingnae
Atopobium
Bifidobacterium longum
Lactobacillus crispatus
Lactobacillus gasseri
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Megasphaera micronuciformis
Prevotella sp. oral taxon 313
Rothia mucilaginosa
Streptococcus sp. oral taxon 057
Streptococcus sp. oral taxon 070
Treponema denticola
Actinomycetota
Lancefieldella parvula

Revision editor(s): Nnadichioma, Aiyshaaaa

Signature 2

Needs review

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa

Source: Table 3 and 4

Description: Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: decreased abundance in Current-Smokers

NCBI Links
Aggregatibacter
Capnocytophaga sputigena
Enterococcus
Gemella
Haemophilus parahaemolyticus
Haemophilus paraphrohaemolyticus
Kingella denitrificans
Lachnoanaerobaculum umeaense
Lachnospiraceae
Lautropia
Neisseria
Neisseria oralis
Neisseria pharyngis
Neisseria pharyngis subsp. flava
Prevotella nanceiensis DSM 19126 = JCM 15639
Pseudomonadota
[Eubacterium] infirmum
Kingella elongataKingella elongata
Streptococcus cristatus

Revision editor(s): Nnadichioma, Aiyshaaaa