Lower respiratory tract microbiome composition and community interactions in smokers/Experiment 2
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
- Never smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- former smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects that are abstinent of tobacco use for at least 12months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- 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).
- 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
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 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers vs former smokers using DESeq2.
Abundance in Group 1: increased abundance in former smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Ralstonia sp. 1-6 |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers vs former smokers using DESeq2.
Abundance in Group 1: increased abundance in former smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Lautropia | ||
| Leptotrichia | ||
| Prevotella sp. |
Revision editor(s): OdigiriGreat, Folakunmi
