Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia/Experiment 3
From BugSigDB
Needs review
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
- Cecum mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Social environment measurement Social environment measurement,social environment measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Enterotype 1 + Enterotype 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Enterotype 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Enterotype 3 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 3. They were particularly distinct from enterotypes 1 and 2 and clearly dominated by Climate zone 1.
- Group 1 sample size Number of subjects in the case (exposed) group
- 148
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
- 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
- 4
Signature 1
Needs review
Source: Fig. 3C
Description: Differential enrichment of genera between enterotypes using LEfSe analysis
Abundance in Group 1: increased abundance in Enterotype 3
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Megamonas | ||
| Faecalibacterium | ||
| Olsenella | ||
| Lactobacillus | ||
| Bifidobacterium | ||
| Mediterranea | ||
| Collinsella | ||
| Megasphaera | ||
| Dialister |
Revision editor(s): KateRasheed
