Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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 diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Test diet
- 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 with average water temperature of 3.9, 3.4 and 9.6 degree celsius 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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)
- 0.05
- 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
- Richness Number of species
- unchanged
Signature 1
Source: General Performance
Description: Effects of diets containing yeast cell-wall based prebiotics on the gut microbiota of Atlantic Salmon in September: Mycoplasma became more prominent as fish progressed towards April and September.
Abundance in Group 1: increased abundance in Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Mycoplasma |
Revision editor(s): Bolanle
Signature 2
Source: Supplementary material 3
Description: Relative abundance of all Amplicon sequence variants (ASVs) for each sample; life stage dietary treatmet LAB decreasing trend suggests a change in the gut microbiome composition of Atlantic Salmon in response to diets
Abundance in Group 1: decreased abundance in Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactococcus | ||
| Leuconostoc |
Revision editor(s): Bolanle
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- January Reference diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- January Test diet
- 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
Statistical Analysis
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 7
Description: most abundant taxa at genus level of all samples relative abundance of each taxon
Abundance in Group 1: increased abundance in January Test diet
Revision editor(s): Bolanle
Signature 2
Source: Figure 7
Description: most abundant taxa at genus level of all samples relative abundance of each taxon
Abundance in Group 1: decreased abundance in January Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Ureibacillus |
Revision editor(s): Bolanle
Experiment 3
Subjects
- 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 April
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
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
Source: FIgure 7
Description: Compared to January fish, April fish showed a slight increase in genera Proteobacteria (15% and 10% in Reference fed and Test-fed fish, respectively) and Mycoplasma (4% and 29.5% in Reference fed and Test- fed fish, respectively)
Abundance in Group 1: increased abundance in Fishes fed with test diet in April
| NCBI | Quality Control | Links |
|---|---|---|
| Photobacterium |
Revision editor(s): Bolanle
Experiment 4
Subjects
- 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
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
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
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 |
Revision editor(s): Bolanle
Signature 2
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 |
Revision editor(s): Bolanle
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- April Reference diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- April Test diet
- 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 with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 7
Description: most abundant taxa at genus level of all samples relative abundance of each taxon
Abundance in Group 1: increased abundance in April Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Halomonas | ||
| Mycoplasma | ||
| Shewanella | ||
| Weissella | ||
| Oscillospiraceae bacterium | ||
| Aliivibrio |
Revision editor(s): Bolanle
Signature 2
Source: Figure 7
Description: most abundant taxa at genus level of all samples relative abundance of each taxon
Abundance in Group 1: decreased abundance in April Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Leuconostoc | ||
| Lactococcus | ||
| Peptostreptococcaceae | ||
| Peptostreptococcus | ||
| Bacillus | ||
| Ureibacillus | ||
| Photobacterium | ||
| Psychrilyobacter | ||
| Clostridium |
Revision editor(s): Bolanle
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- september Reference diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- september Test diet
Lab analysis
Statistical Analysis
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 7
Description: most abundant taxa at genus level of all samples relative abundance of each taxon
Abundance in Group 1: increased abundance in september Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Ureibacillus | ||
| Photobacterium | ||
| Lactobacillus | ||
| Shewanella | ||
| Psychrilyobacter |
Revision editor(s): Bolanle
Signature 2
Source: Figure 7
Description: most abundant taxa at genus level of all samples relative abundance of each taxon
Abundance in Group 1: decreased abundance in september Test diet
| NCBI | Quality Control | Links |
|---|---|---|
| Halomonas | ||
| Mycoplasma |
Revision editor(s): Bolanle
