Comparison of the respiratory microbiome in healthy nonsmokers and smokers/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
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
- Smoking behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy current smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who currently smoke.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No use of antibiotics in the past 3 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, sex, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3B and Figure 4B
Description: Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.
Abundance in Group 1: decreased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Lactobacillales | ||
| Neisseria | ||
| Oribacterium | ||
| Porphyromonas | ||
| Prevotella | ||
| Rothia | ||
| Streptococcus | ||
| Veillonella | ||
| Fusobacterium | ||
| Gemella | ||
| Bacteroidales bacterium |
Revision editor(s): Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3B and Figure 4B
Description: Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.
Abundance in Group 1: increased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Fusobacterium | ||
| Oribacterium | ||
| Pasteurellaceae | ||
| Prevotella | ||
| Tropheryma | ||
| Streptococcus |
Revision editor(s): Atrayees, ChiomaBlessing
