Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-31
Curated date: 2023/04/03
Curator: Khadeeejah
Revision editor(s): Claregrieve1, Khadeeejah, Atrayees, Aiyshaaaa
Subjects
- Location of subjects
- Jordan
- 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
- Non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Smoking subjects who smoked at least one cigarette per day.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 49
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-31
Source: Table 3, 4
Description: Differential microbial abundance between non-smokers versus smokers (regardless of gender).
Abundance in Group 1: increased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Fusobacteriia | ||
| Prevotella | ||
| Pseudomonadota | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Khadeeejah, Atrayees, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-31
Source: Table 3, 4
Description: Differential microbial abundance between non-smokers versus smokers (regardless of gender).
Abundance in Group 1: decreased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria |
Revision editor(s): Khadeeejah, Atrayees, Claregrieve1
