Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Curated date: 2024/03/14
Curator: Bolanle
Revision editor(s): WikiWorks, Bolanle, Omojokunoluwatomisin
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
- Fishes fed with test diet in January
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fishes fed with test diet in September
- 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 September
- 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
- 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).
- relative abundances
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 7
Description: As fish subject progressed towards september, Mycoplasma (50% and 47% in Reference diet fish and Test dit fish respectively) became more prominent.
Abundance in Group 1: increased abundance in Fishes fed with test diet in September
| NCBI | Quality Control | Links |
|---|---|---|
| Mycoplasma |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 7
Description: there was reduction in Lactic acid bacteria(LAB), for example Lactobacillus (12%), Leuconostoc (0.03%) and Lactococcus(0.02%) in Reference diet fish, and Lactobacillus (12%), Leuconostoc (0.05%) and Lactococcus (0.02%) in Test diet fish, respectively.
Abundance in Group 1: decreased abundance in Fishes fed with test diet in September
| NCBI | Quality Control | Links |
|---|---|---|
| Leuconostoc | ||
| Lactobacillus | ||
| Lactococcus |
