NFR 248792
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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About the DigiSal project
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.
Connected to
The national consortium for biotechnology, Centre for Digital Life NorwayObjectives
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.
- Provide and validate a framework for a model-based account of genetic and environmental variation in salmon metabolism
- Unravelling the systemic role of gut microbiota in adapting to new feeds
- Provide and validate a theoretical framework for systematic identification of targets for steering EPA/DHA metabolism through concerted use of nutrition and genetics
- Provide the foundation for a Digital Salmon knowledge base enabling adaption of a transformative pre-emptive research and development strategy
DigiSal is part of the Digital Life Norway, the national centre for biotechnology research, education and innovation, funded by the Research Council of Norway.
DigiSal in the news
- Sjå korleis laksen kan bli vegetarianar (forskning.no animasjon 2018-01-05)
- Den digitale laksen (Dagens Næringsliv 2017-12-30)
- Anvendt science fiction (Forskningsdagenes podcast 2017-09-14)
- Den digitale laksen (Genialt 2/2017 side 6)
- Storsatsing innen bioteknologi: Senter for digitalt liv Norge (DLN) (Tekna Biotek 2016-06-16, opptak fra arrangementet fins nede på siden. DigiSal starter 50 minutt uti sendingen.)
- The fishy biotech future (Norway Exports - Seafood, Fishing & Aquaculture 2016/2017: page 30-31)
- Nasjonalt senter for digitalt liv viser vei mot fremtiden (NBS-nytt 2015/4, tidsskrift for Norsk Biokjemisk Selskap)
- First tailbeats of the Digital Salmon (iScience blog 2015-10-22)
- NMBU-forsker: -Nå er vi på landslaget i bioteknologi (Østlandets Blad 2015-10-14, subscription required)
- NOK 250 million for a new biotechnology centre (Research Council of Norway 2015-10-07)
- Nyvinnende forskningsprosjekt vil bidra til mer bærekraftig oppdrettsnæring | Norges miljø- og biovitenskapelige universitet (NMBU 2015-10-02)
- NMBU tildelt millionprosjekt under nytt nasjonalt senter for bioteknologi (NMBU 2015-09-30)
- Kjempeløft for bioteknologi, skal hjelpe Norge på vei når oljen svikter (Aftenposten 2015-09-30)
Participants
External participants
Fabian Grammes - Associated scientist
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.
Publications
SALARECON connects the Atlantic salmon genome to growth and feed efficiency
Zakhartsev et al, PLOS Computational Biology, 2022Diet and Life Stage-Associated Lipidome Remodeling in Atlantic Salmon
Jin et al, Journal of Agricultural and Food Chemistry, 2021MEMOTE for standardized genome-scale metabolic model testing
Lieven et al, Nature Biotechnology, 2020Targeted mutagenesis of Δ5 and Δ6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)
Jin et al, BMC Genomics, 2020Comparative transcriptomics reveals domestication‐associated features of Atlantic salmon lipid metabolism
Jin et al, Molecular Ecology, 2020Liver slice culture as a model for lipid metabolism in fish
Harvey et al, PeerJ, 2019CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Datsomor et al, Scientific Reports, 2019The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation
van Dam et al, Scientific Data, 2019Transcriptional regulation of lipid metabolism when salmon fry switches from endogenous to exogenous feeding
Jin et al, Aquaculture, 2019Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon
Gillard et al, Molecular Ecology, 2018A systemic study of lipid metabolism regulation in salmon fingerlings and early juveniles fed plant oil
Jin et al, British Journal of Nutrition, 2018Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry
Jin et al, BMC Genomics, 2018A stable core gut microbiota across freshwater-to-saltwater transition for farmed Atlantic salmon
Rudi et al, Applied and Environmental Microbiology, 2017
Macqueen et al, BMC Genomics, 2017