Study 919

From BugSigDB
incomplete
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Journal
Year

Experiment 1


Needs review

Curated date: 2024/03/08

Curator: Bolanle

Revision editor(s): Bolanle

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

Needs review

Curated date: 2024/03/08

Curator: Bolanle

Revision editor(s): Bolanle

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 ControlLinks
Mycoplasma

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/11

Curator: Bolanle

Revision editor(s): Bolanle

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 ControlLinks
Lactobacillus
Lactococcus
Leuconostoc

Revision editor(s): Bolanle