Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models/Experiment 8

From BugSigDB


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
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
TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
TAC-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 Taconic Farms (TAC-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
increased

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3O

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in TAC-CH group

NCBI Quality ControlLinks
Turicibacter

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3O

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in TAC-CH group

NCBI Quality ControlLinks
Gammaproteobacteria

Revision editor(s): Aleru Divine