Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes/Experiment 2
From BugSigDB
Subjects
- Location of subjects
- Ethiopia
- 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
- Restricted to specific location localized,Restricted to specific location,restricted to specific location
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Amhara (AM) highland region
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Afar (AF) lowland region
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Afar (AF) is a low altitude region known for active volcanic eruptions and receives relatively limited rainfall (Dulecha, 730 m above sea level).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Figure S1
Description: Taxa differentially abundant between AM(Amhara: highland region) and AF(Afar: lowland region).
Abundance in Group 1: increased abundance in Afar (AF) lowland region
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides sp. CAG:661 | ||
| Coprobacter secundus |
Revision editor(s): Tosin
Signature 2
Source: Figure S1
Description: Taxa differentially abundant between AM(Amhara: highland region) and AF(Afar: lowland region).
Abundance in Group 1: decreased abundance in Afar (AF) lowland region
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides sp. An51A | ||
| Bacteroides sp. CAG:462 | ||
| Clostridiales bacterium CHKCI006 | ||
| Faecalibacterium sp. An121 |
Revision editor(s): Tosin
