Effects of smoking on the lower respiratory tract microbiome in mice/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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 behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-smoking
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smoking
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male Kunming mice exposed to smoking for 2h per day for 90 days.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NA
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Figure 10
Description: Differential microbial abundance between the smoking and non-smoking mice
Abundance in Group 1: increased abundance in Smoking
Revision editor(s): Sophy, Aiyshaaaa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Figure 10
Description: Differential microbial abundance between the smoking and non-smoking mice
Abundance in Group 1: decreased abundance in Smoking
Revision editor(s): Sophy, Claregrieve1
