Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome/Experiment 4
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
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mice exposed to smoke
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- male, female or ovariectomized females mice exposed to smoke
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
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
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 2
Description: Differential microbial taxa between the control and smoke-exposed groups
Abundance in Group 1: increased abundance in mice exposed to smoke
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Akkermansia sp. | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Oscillibacter | ||
| Verrucomicrobiia | ||
| Verrucomicrobiales | ||
| Verrucomicrobiota |
Revision editor(s): Claregrieve1, WikiWorks, Merit
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Curated date: 2021/01/10
Curator: Zyaijah Bailey
Revision editor(s): WikiWorks, Claregrieve1, Merit, Atrayees
Source: Figure 2
Description: Differential microbial taxa between the control and smoke-exposed groups
Abundance in Group 1: decreased abundance in mice exposed to smoke
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Lachnospiraceae | ||
| Muribaculaceae | ||
| Rikenellaceae | ||
| uncultured Bacteroidales bacterium | ||
| Lachnospira | ||
| Lachnospira sp. |
Revision editor(s): WikiWorks, Claregrieve1, Merit, Atrayees
