Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice/Experiment 2
From BugSigDB
Needs review
Subjects
- Location of subjects
- Czechia
- 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
- Vagina , Saliva Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fertilized ovule stage Fertilized ovule stage,fertilized ovule stage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Oral (saliva) sample
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vagina sample
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- vagina sample collected
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- ANCOM
- Random Forest Analysis
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 5d
Description: Random Forest determined bacterial genera in oral (B) and vaginal (D) samples, which are important for the classification of data into four phases of the cycle.
Abundance in Group 1: increased abundance in Vagina sample
| NCBI | Quality Control | Links |
|---|---|---|
| Massilia | ||
| muribactermuribacter |
Revision editor(s): Omojokunoluwatomisin
Signature 2
Needs review
Source: Figure 5b
Description: Random Forest determined bacterial genera in oral (B) and vaginal (D) samples, which are important for the classification of data into four phases of the cycle.
Abundance in Group 1: decreased abundance in Vagina sample
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Rodentibacter |
Revision editor(s): Omojokunoluwatomisin
