Cigarette smoking and the oral microbiome in a large study of American adults/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1

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
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 behavior smoking,Smoking behavior,smoking behavior
Group 0 name Corresponds to the control (unexposed) group for case-control studies
former smoker
Group 1 name Corresponds to the case (exposed) group for case-control studies
current smoker
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples
Group 0 sample size Number of subjects in the control (unexposed) group
521
Group 1 sample size Number of subjects in the case (exposed) group
112

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
Roche454

Statistical Analysis

Statistical test
Kruskall-Wallis
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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): Claregrieve1, WikiWorks

Source: Table 2

Description: Differential microbial abundance between current and former smokers

Abundance in Group 1: increased abundance in current smoker

NCBI Quality ControlLinks
Actinomycetota
Coriobacteriia

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): Claregrieve1, WikiWorks

Source: Table 2

Description: Differential microbial abundance between current and former smokers

Abundance in Group 1: decreased abundance in current smoker

NCBI Quality ControlLinks
Betaproteobacteria
Flavobacteriia
Gammaproteobacteria
Pseudomonadota

Revision editor(s): Claregrieve1, WikiWorks