The subgingival microbiome of clinically healthy current and never smokers/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-3-28
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
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque
- 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
- Never 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
- people who are current smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
- 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
- V1-V9
- 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
- T-Test
- 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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, education level, race, sex, socioeconomic status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-3-28
Curated date: 2023/03/14
Curator: Kelvin Joseph
Revision editor(s): Kelvin Joseph, Claregrieve1, WikiWorks
Source: Text
Description: The relative abundance of selected species in current smokers and nonsmokers.
Abundance in Group 1: increased abundance in Healthy Current Smokers
Revision editor(s): Kelvin Joseph, Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-3-28
Curated date: 2023/03/14
Curator: Kelvin Joseph
Revision editor(s): Kelvin Joseph, Claregrieve1, WikiWorks
Source: Text
Description: The relative abundance of selected species in current smokers and nonsmokers.
Abundance in Group 1: decreased abundance in Healthy Current Smokers
Revision editor(s): Kelvin Joseph, Claregrieve1, WikiWorks
