Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models/Experiment 7
From BugSigDB
Needs review
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
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- JAX group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JAX-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 3N
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Dehalobacterium | ||
| Mucispirillum | ||
| Parabacteroides |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 3N
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Bifidobacterium | ||
| Muribaculaceae | ||
| Rikenellaceae | ||
| Staphylococcus |
Revision editor(s): Aleru Divine
