Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-23
Subjects
- Location of subjects
- Italy
- 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
- 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,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking status measurement 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
- Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 880
- Group 1 sample size Number of subjects in the case (exposed) group
- 326
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 12 weeks
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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, number of teeth measurement, 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-22
Source: figure 1
Description: Heatmap of the 44 genera diferentially abundant between Current and Never smokers
Abundance in Group 1: increased abundance in Current smokers
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-22
Source: figure 1
Description: Result of the Heatmap of the 44 genera diferentially abundant between Current and Never smokers.
Abundance in Group 1: decreased abundance in Current smokers
Revision editor(s): OdigiriGreat, Folakunmi
