The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production/Experiment 3
From BugSigDB
Subjects
- Location of subjects
- Norway
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Salmo salar
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Actinopterygian pyloric caecum Pyloric appendage,Pyloric caeca,Pyloric caecum,Actinopterygian pyloric caecum,actinopterygian pyloric caecum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to diet Response to diet,response to diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 4% CTR Diet Pyloric caecum
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 4% MN3 Pyloric caecum
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Salmon fed with a standard commercial diet supplemented with 4% MN3 ( 4% w/w acetylated β-galactoglucomannan) for 4 weeks.
- 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
- 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
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 2F
Description: Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the pyloric caecum of salmons fed a 4% MN3 diet or a CTR diet.
Abundance in Group 1: increased abundance in 4% MN3 Pyloric caecum
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Pseudomonas | ||
| Burkholderia/Caballeronia/Paraburkholderia groupBurkholderia/Caballeronia/Paraburkholderia group |
Revision editor(s): YokoC
Signature 2
Source: Fig. 2F
Description: Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the pyloric caecum of salmons fed a 4% MN3 diet or a CTR diet.
Abundance in Group 1: decreased abundance in 4% MN3 Pyloric caecum
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Gallicola | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Limosilactobacillus | ||
| Peptostreptococcus | ||
| Tepidimicrobium |
Revision editor(s): YokoC
