Systems biology will aid sustainability in salmon farming. Scarcity of fish oil has forced development of novel feedstuffs, challenging the salmon's metabolism as well as our understanding of it.
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Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted whole.
DigiSal will focus on challenges of novel feedstuffs, collaborating with the Foods of Norway centre for research-based innovation at NBMU. Salmon are carnivores but today aquaculture provides more than half their fat and protein from plants, challenging the metabolic system and affecting fish health and nutritional value of salmon meat. The newly sequenced salmon genome and related resources will enable a tightly integrated theoretical-experimental study of mechanistic interactions among genetic and feed factors.
Systems-oriented mathematical and statistical modelling will be central, using existing and novel knowledge e.g. on metabolic reaction networks to guide design of experiments through multiple iterations. Metabolic function of fish will be characterized via multiple omics technologies in feeding trials and in vitro tissue-slice culture. Gut microbiota will receive particular attention. The resulting massive data will be summarized via multivariate models to deliver a predictive understanding of a whole range of possible diets, much more efficiently than by traditional feeding trials alone. Data and models will be annotated using bio-relevant ontologies, so that new knowledge automatically connects to that which already exists. Future challenges will be met by quickly reanalysing existing information and understanding of salmon biology, identifying knowledge gaps, acquiring new data and incorporating it into a unified whole. Thus, we begin a shift from a reactive to a pre-emptive R&D strategy in aquaculture.
Project objective: Establish a systems biology framework for adapting salmon breeding and nutrition strategies to modern feedstuffs, blazing the trail for a Digital Salmon endeavour.
DigiSal is part of the Digital Life Norway, the national centre for biotechnology research, education and innovation, funded by the Research Council of Norway.
SALARECON connects the Atlantic salmon genome to growth and feed efficiencyZakhartsev et al, PLOS Computational Biology, 2022
Diet and Life Stage-Associated Lipidome Remodeling in Atlantic SalmonJin et al, Journal of Agricultural and Food Chemistry, 2021
MEMOTE for standardized genome-scale metabolic model testingLieven et al, Nature Biotechnology, 2020
Targeted mutagenesis of Δ5 and Δ6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)Jin et al, BMC Genomics, 2020
Comparative transcriptomics reveals domestication‐associated features of Atlantic salmon lipid metabolismJin et al, Molecular Ecology, 2020
Liver slice culture as a model for lipid metabolism in fishHarvey et al, PeerJ, 2019
CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genesDatsomor et al, Scientific Reports, 2019
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotationvan Dam et al, Scientific Data, 2019
Transcriptional regulation of lipid metabolism when salmon fry switches from endogenous to exogenous feedingJin et al, Aquaculture, 2019
Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmonGillard et al, Molecular Ecology, 2018
A systemic study of lipid metabolism regulation in salmon fingerlings and early juveniles fed plant oilJin et al, British Journal of Nutrition, 2018
Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fryJin et al, BMC Genomics, 2018
A stable core gut microbiota across freshwater-to-saltwater transition for farmed Atlantic salmon
Rudi et al, Applied and Environmental Microbiology, 2017
Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture
Macqueen et al, BMC Genomics, 2017
Postdoc, systems biology.
PhD student, biotechnology/metabolic modelling.
Postdoc, lipid physiology.
Scientific coordinator. Leader of WP3: Omics and imaging. RNA sequencing expert.
Leader of WP1: Feeding trials. Heads the nutrition part of Foods of Norway, with which DigiSal interfaces closely.
Leader of WP4: Genomics. Salmon genome guru.
Head of the ELIXIR node at NMBU, focusing on the salmon genome.
Head of Foods of Norway.
AquaGen (salmon breeding company)
Dr. Jacob Torgersen, leader of WP2: In vitro studies. Molecular biologist.
Dr. Nina Santi, research director of AquaGen.
Norwegian University of Science and Technology
Prof. Per Bruheim, metabolomicist.
Dr. Zdenka Bartosova, metabolomicist.
Dr. Marit Hallvardsdotter Stafsnes, metabolomicist.
Dr. Per Winge, gene editor.
Prof. Trygve Brautaset, systems biologist.
Prof. Stig Omholt, visionary.
University of Bergen
Dr. Eivind Valen, bioinformatician.
Prof. Inge Jonassen, bioinformatician.
Institute for marine research
Dr. Anna Wargelius, functional genomicist.
Dr. Rolf Edvardsen, molecular biologist.
University of Stirling
Prof. Michael Leaver, fish-nutritional geneticist.
Wageningen University and Research Centre
Systems and synthetic biology group:
Prof. Vítor Martins dos Santos.
Prof. Peter Schaap.
Dr. María Suárez-Diez.
Dr. Jasper Koehorst.
EWOS (feed producer)
FAIRDOM (consortium for findable, accessible, interoperable and reusable data, operations and models)
Dr. Stuart Owen, director of technical development.
Project leader and leader, systems biologist.
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