Oral microbiome and history of smoking and colorectal cancer/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-6-7
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,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,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non 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 smokers, where defined as ever smokers who smoked at least one cigarette per day for six months or longer and were smoking within 2 year prior to interview.
- 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
- 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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Negative Binomial Regression
- Zero-Inflated Beta Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- region of residence, race, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, smoking status
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
Reviewed Marked as Reviewed by Lwaldron on 2023-6-7
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 | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Clostridiales bacterium | ||
| Veillonellaceae | ||
| Veillonella | ||
| Veillonella atypica | ||
| Bacteroidia | ||
| Actinomycetota |
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2023-6-7
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 | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Betaproteobacteria | ||
| Neisseriales | ||
| Neisseriaceae | ||
| Neisseria | ||
| Neisseria mucosa | ||
| Fusobacteriia |
