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

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Reviewed Marked as Reviewed by Atrayees on 2023-6-1
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
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
Keywords:
African-American, European-American, cigarette smoking, oral microbiota
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


Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Fiddyhamma

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
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
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, alcohol drinking, body mass index, race, sex, 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, oral hygiene

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Atrayees, Aiyshaaaa, Merit

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 Quality ControlLinks
Bifidobacteriaceae
Bifidobacterium
Bifidobacterium longum
Lactobacillus
Lactobacillus crispatus
Lactobacillus gasseri
Lancefieldella parvula
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Actinomycetota
Actinomycetaceae
Actinomyces
Actinomyces graevenitzii
Rothia
Schaalia odontolytica
Coriobacteriaceae
Rothia mucilaginosa
Atopobium
Prevotella sp. oral taxon 313
Streptococcus sp. oral taxon 057
Megasphaera
Megasphaera micronuciformis
Actinomyces lingnae
Lactobacillaceae
Treponema denticola

Revision editor(s): Nnadichioma, Atrayees, Aiyshaaaa, Merit

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

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 Quality ControlLinks
Burkholderiaceae
Cardiobacterium
Enterococcus
Kingella
Kingella denitrificans
Lautropia
Neisseria
Neisseria oralis
Neisseriaceae
Hoylesella nanceiensis
Capnocytophaga sputigena
Lachnospiraceae
[Eubacterium] infirmum
Lachnoanaerobaculum umeaense
Pseudomonadota
Neisseria pharyngis
Neisseria subflava
Pasteurellaceae
Aggregatibacter
Haemophilus
Haemophilus parahaemolyticus
Haemophilus paraphrohaemolyticus
Flavobacteriaceae
Gemella
Streptococcus cristatus

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Former-Smokers
Group 1 sample size Number of subjects in the case (exposed) group
477

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Merit, 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 relative abundance between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Former-Smokers

NCBI Quality ControlLinks
Bifidobacterium
Bifidobacterium longum
Lactobacillus crispatus
Lactobacillus gasseri
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Streptococcus sp. oral taxon 057
Actinomycetaceae
Actinomycetota
Rothia
Rothia mucilaginosa
Haemophilus parahaemolyticus
Streptococcus cristatus
Actinomyces lingnae
Bifidobacteriaceae

Revision editor(s): Nnadichioma, Aiyshaaaa, Merit, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Source: Table 2, 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 Quality ControlLinks
Capnocytophaga sputigena
Cardiobacterium
Enterococcus
Kingella denitrificans
Lachnoanaerobaculum umeaense
Lachnospiraceae
Lautropia
Neisseria oralis
Streptococcus sp. oral taxon 070
Treponema denticola
[Eubacterium] infirmum
Burkholderiaceae
Kingella
Prevotella
Lactobacillaceae
Actinomyces graevenitzii
Coriobacteriaceae
Atopobium
Lancefieldella parvula
Haemophilus
Aggregatibacter
Pseudomonadota
Neisseria
Neisseriaceae
Neisseria pharyngis
Neisseria subflava
Pasteurellaceae
Haemophilus paraphrohaemolyticus
Gemella
Streptococcus cristatus

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Fiddyhamma

Differences from previous experiment shown

Subjects

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 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

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, 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 relative abundance between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Current-Smokers

NCBI Quality ControlLinks
Actinomyces
Actinomyces graevenitzii
Actinomyces lingnae
Actinomycetota
Atopobium
Bifidobacterium longum
Lactobacillus crispatus
Lactobacillus gasseri
Lancefieldella parvula
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
Lactobacillaceae
Bifidobacterium
Rothia
Megasphaera
Lactobacillus

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Merit, Atrayees

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 Quality ControlLinks
Aggregatibacter
Capnocytophaga sputigena
Enterococcus
Gemella
Haemophilus parahaemolyticus
Haemophilus paraphrohaemolyticus
Kingella denitrificans
Lachnoanaerobaculum umeaense
Lachnospiraceae
Lautropia
Neisseria
Neisseria elongata
Neisseria oralis
Neisseria pharyngis
Neisseria pharyngis subsp. flava
Hoylesella nanceiensis DSM 19126 = JCM 15639
Pseudomonadota
Streptococcus cristatus
[Eubacterium] infirmum
Neisseriaceae
Haemophilus
Pasteurellaceae
Flavobacteriaceae
Burkholderiaceae
Kingella
Cardiobacterium

Revision editor(s): Nnadichioma, Aiyshaaaa, Merit, Atrayees