Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Gallus gallus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Growth rate measurement Growth rate measurement,growth rate measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low feed efficiency (LFE)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High feed efficiency (HFE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Yellow broilers with low feed conversion ratio (FCR).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of 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 5
Description: LEfSe results for cecal microbiota of HFE and LFE groups.
Abundance in Group 1: increased abundance in High feed efficiency (HFE)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 5
Description: LEfSe results for cecal microbiota of HFE and LFE groups.
Abundance in Group 1: decreased abundance in High feed efficiency (HFE)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Rikenellaceae |
Revision editor(s): Aleru Divine
