Comparison of the respiratory microbiome in healthy nonsmokers and smokers/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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
Middle lobe of lung Lung middle lobe,Middle lobe of lung,middle lobe of lung
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
V1-V3
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
decreased
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
increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

Source: Figure 3A

Description: Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.

Abundance in Group 1: decreased abundance in Healthy current smokers

NCBI Quality ControlLinks
Fusobacterium
Gemella
Granulicatella
Haemophilus
Neisseria
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

Source: Figure 3A

Description: Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.

Abundance in Group 1: increased abundance in Healthy current smokers

NCBI Quality ControlLinks
Actinomyces
Heterosigma akashiwo
Veillonella

Revision editor(s): Atrayees, ChiomaBlessing