Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Subjects
- Location of subjects
- Canada
- 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
- Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Air pollution air pollution,Air pollution
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- all other mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- female mice exposed to cigarette smoke
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- female mice exposed to cigarette smoke
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 7
Description: Differentially abundant taxa in the smoke-exposed female mice versus all other mice
Abundance in Group 1: increased abundance in female mice exposed to cigarette smoke
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Muribaculaceae |
Revision editor(s): WikiWorks, Claregrieve1
