Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models/Experiment 11
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
- Feces , Colon Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces,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
- TAC-CH colon group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TAC-CH fecal pellets group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- 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
Signature 1
Needs review
Source: Figure S3
Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).
Abundance in Group 1: increased abundance in TAC-CH fecal pellets group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Akkermansia | ||
| Bacteroides | ||
| Bifidobacterium | ||
| Clostridiaceae | ||
| Erysipelotrichaceae | ||
| Lactobacillus | ||
| Muribaculaceae | ||
| Parabacteroides | ||
| Rickettsiales | ||
| RF39RF39 |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure S3
Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).
Abundance in Group 1: decreased abundance in TAC-CH fecal pellets group
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Mucispirillum | ||
| Anaeroplasma | ||
| Oscillospiraceae | ||
| Oscillospira | ||
| Ruminococcus | ||
| Ruminococcus sp. | ||
| Coprococcus |
Revision editor(s): Aleru Divine
