The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production
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Study information
incomplete
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Gupta S, Vera-Ponce de León A, Kodama M, Hoetzinger M, Clausen CG, Pless L, Verissimo ARA, Stengel B, Calabuig V, Kvingedal R, Skugor S, Westereng B, Harvey TN, Nordborg A, Bertilsson S, Limborg MT, Mørkøre T, Sandve SR, Pope PB, Hvidsten TR, La Rosa SL
Journal
Communications biology
Year
2024
Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on α-mannooligosaccharides (MOS) and β-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two α-mannans and an acetylated β-galactoglucomannan), at a dose of 0.2% in the diet, had negligible effects on both host gene expression, and gut microbiome structure and function under the studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of β-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of β-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline previously unreported and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon.
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
- Hindgut Metenteron,Hindgut,hindgut
- 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
- 0.2% CTR T2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 0.2% MC2 T2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Salmon fed a standard commercial diet supplemented with MC2 (a 0.2% w/w α-mannan supplement produced by Cargill) at 10 weeks (T2, smolt stage) after the experiment started.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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. 1G
Description: Statistically significant differences (Wilcoxon test) between MC2 (Diet 2) and CTR( Control diet) were calculated at 10 weeks (T2, smolt stage) after the experiment began.
Abundance in Group 1: increased abundance in 0.2% MC2 T2
| NCBI | Quality Control | Links |
|---|---|---|
| Cupriavidus | ||
| Herbaspirillum | ||
| Burkholderia/Caballeronia/Paraburkholderia groupBurkholderia/Caballeronia/Paraburkholderia group | ||
| Nitrospirillum |
Revision editor(s): YokoC
Experiment 2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 0.2% MN3 T2
- 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 MN3 (0.2% w/w acetylated β-galactoglucomannan) at 10 weeks (T2, smolt stage) after the experiment started.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Fig. 1G
Description: Statistically significant differences (Wilcoxon test) between MN3 (Diet 3) and CTR( Control diet) were calculated at 10 weeks (T2, smolt stage) after the experiment began.
Abundance in Group 1: increased abundance in 0.2% MN3 T2
| NCBI | Quality Control | Links |
|---|---|---|
| Cupriavidus | ||
| Herbaspirillum | ||
| Nitrospirillum | ||
| Burkholderia/Caballeronia/Paraburkholderia groupBurkholderia/Caballeronia/Paraburkholderia group |
Revision editor(s): YokoC
Experiment 3
Differences from previous experiment shown
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 4% CTR
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 4% MN3
- 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 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 2F
Description: Statistically significant differences (Wilcoxon test) between MC3 at 4% (Diet 4) and CTR( Control diet).
Abundance in Group 1: increased abundance in 4% MN3
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Pseudomonas | ||
| Burkholderia/Caballeronia/Paraburkholderia groupBurkholderia/Caballeronia/Paraburkholderia group |
Revision editor(s): YokoC
Signature 2
Source: Fig. 2F
Description: Statistically significant differences (Wilcoxon test) between MC3 at 4% (Diet 4) and CTR( Control diet).
Abundance in Group 1: decreased abundance in 4% MN3
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Gallicola | ||
| Lactobacillus | ||
| Peptostreptococcus | ||
| Tepidimicrobium | ||
| Limosilactobacillus | ||
| Lactobacillaceae |
Revision editor(s): YokoC
Experiment 4
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Hindgut Metenteron,Hindgut,hindgut
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Salmon fed a standard commercial diet supplemented with 4% MN3 (4% w/w acetylated β-galactoglucomannan) for 4 weeks.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Fig. 2F
Description: Statistically significant differences (Wilcoxon test) between MC3 4%(Diet 4) and CTR( Control diet).
Abundance in Group 1: increased abundance in 4% MN3
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Pseudomonas | ||
| Burkholderia/Caballeronia/Paraburkholderia groupBurkholderia/Caballeronia/Paraburkholderia group |
Revision editor(s): YokoC
Signature 2
Source: Fig. 2F
Description: Statistically significant differences (Wilcoxon test) between MC2 4%(Diet 4) and CTR( Control diet).
Abundance in Group 1: decreased abundance in 4% MN3
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Lactobacillaceae | ||
| Limosilactobacillus | ||
| Peptostreptococcus | ||
| Streptococcus | ||
| Ligilactobacillus |
Revision editor(s): YokoC
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