Oral microbiome and history of smoking and colorectal cancer

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
Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS, Ram JL
Journal
Journal of epidemiological research
Year
2016
BACKGROUND: The equilibrium of oral microbiome may be altered by environmental factors, including cigarette smoking. Several recent studies also suggest that oral pathogens causing periodontal disease, such as Fusobacterium nucleatum, are involved in pathogenesis of colorectal cancer. METHODS: For this study oral rinse DNA samples from 190 participants in a population-based case-control study for colorectal cancer were used to amplify a V3-V4 region of bacterial 16S rRNA gene. The amplicons were sequenced using Illumina MiSeq paired end chemistry on two runs, yielding approximately 35 million filtered reads which were assigned to bacterial phyla. RESULTS: No association was found between Fusobacterium abundance or presence and colorectal cancer. However, adjusted for age and experimental batch, colorectal cancer history was associated with increased presence of genus Lactobacillus and increased relative abundance of Rothia by 28% and current smoking was associated with a 33% decrease in relative counts of Betaproteobacteria (primarily Neisseria) and 23% increase in relative abundance of Veillonellaceae family. We also found that smoking had significant effects on the 2nd component scores and 2nd coordinate distances in principal component and coordinate analyses. CONCLUSIONS: It remains to be elucidated whether the observed differences can be translated into biochemical changes in oral environment, thus potentially affecting oral health.

Experiment 1


Needs review

Curated date: 2022/07/28

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine
Group 0 name Corresponds to the control (unexposed) group for case-control studies
controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colorectal cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
colorectal cancer; 24% of the colorectal cancer cases were current smokers. 16% habitual alcohol drinkers
Group 0 sample size Number of subjects in the control (unexposed) group
122
Group 1 sample size Number of subjects in the case (exposed) group
68
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None specified

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Zero-Inflated Beta Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
race, sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Experiment 2


Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine
Group 0 name Corresponds to the control (unexposed) group for case-control studies
controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colorectal cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
colorectal cancer; 24% of the colorectal cancer cases were current smokers. 16% habitual alcohol drinkers
Group 0 sample size Number of subjects in the control (unexposed) group
122
Group 1 sample size Number of subjects in the case (exposed) group
68
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None specified

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
race, 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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Table 3

Description: The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models

Abundance in Group 1: increased abundance in Colorectal cancer

NCBI Links
Rothia
Lactobacillus

Revision editor(s): Jeshudy

Experiment 3


Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Young
Group 1 name Corresponds to the case (exposed) group for case-control studies
Old (≥ 65 yrs)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
65+, regardless of cancer status
Group 0 sample size Number of subjects in the control (unexposed) group
103
Group 1 sample size Number of subjects in the case (exposed) group
87
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None specified

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
race, 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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Table 3

Description: The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models

Abundance in Group 1: increased abundance in Old (≥ 65 yrs)

NCBI Links
Streptococcus gordonii
Porphyromonas gingivalis

Revision editor(s): Jeshudy

Experiment 4


Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non, Ex 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
Current smoker, regardless of cancer status
Group 0 sample size Number of subjects in the control (unexposed) group
138
Group 1 sample size Number of subjects in the case (exposed) group
52
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None specified

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
race, 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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Table 3

Description: The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models

Abundance in Group 1: decreased abundance in Current Smokers

NCBI Links
Neisseria

Revision editor(s): Jeshudy

Signature 2

Needs review

Curated date: 2022/07/29

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Table 3

Description: The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models

Abundance in Group 1: increased abundance in Current Smokers

NCBI Links
Veillonella atypica

Revision editor(s): Jeshudy