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
- Intestine Bowel,Intestinal tract,Intestine,intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Reference group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Test group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Atlantic Salmon fed with Yeast cell-wall based prebiotics diet in January, April and September with average water temperature of 3.9, 3.4 and 9.6 respectively.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- raw counts
- Statistical test
- ANOVA
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- diet, time
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, body weight, diet, health
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: General Performance
Description: Effects of diets containing yeast cell-wall based prebiotics on the gut microbiota of Atlantic Salmon in September
Abundance in Group 1: increased abundance in Test group
| NCBI | Quality Control | Links |
|---|---|---|
| Mycoplasma |
Revision editor(s): Bolanle
Signature 2
Source: Supplementary material
Description: Relative abundance of all Amplicon sequence variants (ASVs) for each sample; life stage dietary treatmet
Abundance in Group 1: decreased abundance in Test group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactococcus | ||
| Leuconostoc |
Revision editor(s): Bolanle
