Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models/Experiment 18

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Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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
Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
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
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mTAC group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon samples from the maternal F1-generation of Taconic farms (mTAC) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
15
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
Dunn's test
Kruskall-Wallis
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

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
increased
Richness Number of species
increased