Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-4-12
Subjects
- Location of subjects
- South Korea
- 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
- Oviduct Female reproductive tracts,Ovarian duct,Ovarian tube,Oviducts,Tuba uterina,Tuba uterinae,Tubular parts of female reproductive system,Uterine tube,Oviduct,oviduct
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Developmental stage development stage,developmental_stage,life cycle stage,Developmental stage,developmental stage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Immature hen magnum sample (23 weeks-old)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mature hen magnum sample
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Magnum samples of 34 weeks-old laying SPF hens
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V2-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-4-12
Source: Figure 2.
Description: ANCOM differential abundance between the mature and immature hen magnum groups.
Abundance in Group 1: decreased abundance in Mature hen magnum sample
| NCBI | Quality Control | Links |
|---|---|---|
| Bradyrhizobium | ||
| unclassified Bradyrhizobiaceae | ||
| unclassified Nocardiaceae | ||
| Unclassified 0319-6G20Unclassified 0319-6G20 |
