Cigarette smoking and oral microbiota in low-income and African-American populations
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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.
Statistical test
Logistic Regression
Statistical test
Logistic Regression
Statistical test
Logistic Regression
Experiment 1
Needs review
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
- 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
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
Revision editor(s): Nnadichioma, Atrayees
Signature 2
Needs review
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
Revision editor(s): Nnadichioma, Aiyshaaaa
Experiment 2
Needs review
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
- 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
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
Revision editor(s): Nnadichioma, Aiyshaaaa
Signature 2
Needs review
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
Revision editor(s): Nnadichioma, Aiyshaaaa
Experiment 3
Needs review
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
- 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
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
Revision editor(s): Nnadichioma, Aiyshaaaa
Signature 2
Needs review
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
Revision editor(s): Nnadichioma, Aiyshaaaa
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