Lower respiratory tract microbiome composition and community interactions in smokers/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
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
- Lung Pulmo,Lung,lung
- 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
- Active smokers & former smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Never smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who have never smoked
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- use of antibiotics within 12weeks prior to study
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6-V8
- 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
- LEfSe
- 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
- 2.5
Alpha Diversity
- Chao1 Abundance-based estimator of 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
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-13
Source: Fig 5
Description: Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using LEFse.
Abundance in Group 1: increased abundance in Never smokers
Revision editor(s): OdigiriGreat, Folakunmi
