Digital Salmon – from a reactive to a pre-emptive research strategy in aquaculture

Highlights 2020

The project's contribution to the Centre for Digital Life Norway annual report 2020.

Our research in 2020 focused on completing a high-quality metabolic model of Atlantic salmon. Our model captures how enzymatic reactions convert nutrients in the fish feed to the fillet that we eat, and it allows us to connect the Atlantic salmon genome to growth and feed utilisation. It performs very well in standardised tests and captures expected metabolic (in)capabilities of salmon such as amino acid requirements for growth. We are now using modelling to make predictions for aquaculture such as growth-limiting amino acids in current commercial feeds and possible compositions for novel feeds based on sustainable plant-based ingredients.

Besides completing our salmon metabolic model, a major highlight of 2020 was receiving funding for a DigiSal spin-off project where we are extending our modelling efforts to the salmon gut microbiota. In collaboration with other groups at NMBU and the University of Minnesota, we are modelling the spatiotemporal dynamics of microbes in the salmon gut to understand why a specific bacterium becomes dominant when juvenile salmon transition from fresh to salt water.

Being part of a transdisciplinary centre provides us with connections to the systems biology community and industry and helps us see things from a different perspective. It also incentivises collaboration, within projects as well as between different projects (e.g. workshops with the dCod project). Meeting scientists from highly diverse backgrounds, often in informal settings, has been very valuable for us, and it has allowed us to see opportunities for working together with others that we would not have discovered otherwise.

Our model was built from the annotated Atlantic salmon genome, metabolic reaction databases, and literature. The procedure involved (1) manual metabolic reconstruction, (2) semi-automated annotation and curation, and (3) quality evaluation using community-standardised tests and metabolic tasks. Figure credit: Ove Øyås.

Recording of the talk of postdoctoral fellow Ove Øyås at Digital Life 2020 – the annual conference of the Centre for Digital Life Norway

Blog with dCod 1.0: Cross-project collaboration: United fish researchers

Scientific publications 2020: 3

Project overview

Project lead: Jon Olav Vik
Institution: NMBU
Partners: NTNU, UiT, Stirling, Wageningen, Institute of Marine Research, AquaGen, EWOS
Funding: NOK 38.8 mill.
Duration: 2016–2019


Comparative transcriptomics reveals domestication‐associated features of Atlantic salmon lipid metabolism (2020)

Yang Jin, Rolf Erik Olsen, Thomas Nelson Harvey, Mari-Ann Østensen, Keshuai Li, Nina Santi, Olav Vadstein, Atle M. Bones, Jon Olav Vik, Simen Rød Sandve, Yngvar Olsen

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation (2019)

Jesse van Dam, Jasper J Koehorst, Jon Olav Vik, Vitor A.P. Martins dos Santos, Peter J. Schaap, Maria Suarez-Diez

CRISPR/Cas9-mediated editing of Δ5 and Δ6 desaturases impairs Δ8-desaturation and docosahexaenoic acid synthesis in Atlantic salmon (Salmo salar L.) (2019)

Alex Kojo Datsomor, Rolf Erik Olsen, Nikola Zic, Angelico Madaro, Atle M. Bones, Rolf Brudvik Edvardsen, Anna Wargelius, Per Winge

High-throughput method for lipidomic analysis and semi-quantification of lipid classes (2019)

Zdenka Bartosova, Susana Villa Gonzalez, Per Bruheim

Supercritical fluid chromatography with mass spectrometry: A versatile tool for lipid profiling and lipid class quantitation (2019)

Zdenka Bartosova, Marit Hallvardsdotter Stafsnes, Andre Voigt, Per Bruheim

SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes (2019)

Teshome Dagne Mulugeta, Torfinn Nome, Thu-Hien To, Manu Kumar Gundappa, Daniel J. Macqueen, Dag Inge Våge, Simen Rød Sandve, Torgeir Rhoden Hvidsten

Liver slice culture as a model for lipid metabolism in fish (2019)

Thomas Nelson Harvey, Simen Rød Sandve, Yang Jin, Jon Olav Vik, Jacob Seilø Torgersen

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes (2019)

Alex Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge

Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 fatty acids in freshwater have a Mycoplasma-dominated gut microbiota at sea (2019)

Yang Jin, Inga Leena Angell, Simen Rød Sandve, Lars-Gustav Snipen, Yngvar Olsen, Knut Rudi

Transcriptional regulation of lipid metabolism when salmon fry switches from endogenous to exogenous feeding (2018)

Yang Jin, Rolf Erik Olsen, Mari-Ann Østensen, Gareth Benjamin Gillard, Keshuai Li, Thomas Nelson Harvey, Nina Santi, Olav Vadstein, Jon Olav Vik, Simen Rød Sandve, Yngvar Olsen

All results in the CRIStin-database

Research group

Discovering connections between salmon genes and fish feed

Norwegian researchers are developing a mathematical model of the salmon that will make it easier to find the optimal feed for aquaculture production of salmon.

The salmon is a predator which in the wild eats small fish and crustaceans in the ocean, and in the first decenniums of salmon breeding the feeding where based on fish oil and fish meal. But the growth in the business has demanded other feed sources, and today most of the feed are produced on land by farming. 75 percent of the fat and protein in the feed are derived from different plants and crops. This is not a sustainable feed source, and also the prices varies a lot.

The business is therefore investigating alternative feed variants, but to test out which of the many alternatives that are the best choice for salmon is time consuming, with a potential cost of several millions. An additional challenge is that the best feed mixture may vary considerably between different salmon strains.

The researcher know a lot about the salmon genes as the whole salmon genome was fully sequenced and mapped in 2016. They also know a lot about salmon physiology from studying the intestine, liver and muscles. Currently, the aim is to develop a mathematical model for all the processes going on in the fish's different organs, and then fuse it into one coherent model of salmon physiology - the digital salmon. This will then be used to simulate and test different variations of salmon feed, thereby allowing faster and more cost efficient development of better and more sustainable feeds.

Researchers within mathematics, data analysis, informatics, sensor technology, genomics and experimental biologists work together in the project.

The project is headed by the Norwegian University of Life Sciences (NMBU) with partners at NTNU, UiB, UiT,University of Stirling, UK, University of Wagening (The Netherlands), and the Institute of Marine Research (Norway).

Industrial partners are AquaGen (salmon breeding) and EWOS (feed producer).

More about the project

Towards the Digital Salmon

In the project Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal) the researchers will establish a mathematical model of the salmon physiology, to aid the development of tomorrow's salmon feed. The long term vision is to construct the Digital Salmon - a system physiology model where all the salmon's body functions are simulated in a coherent mathematical model. This will be the core in an open access knowledge platform of salmon.

Todays feed composition used for salmon farming is not sustainable. New ingredients are tried out, such as yeast and bacterial extracts, and micro algae. It is, however, a time consuming and expensive process to test out all possible combinations of alternative ingredients in feeding experiments. Also, different salmon strains will most likely respond differently due genetic differences. By replacing initial experiments by simulations, a more cost effective and improved feed development can be established.

Utilizing the salmon genome

The researcher will therefore translate knowledge about salmon physiology into mathematical expressions. The underlying biochemical pathways are tightly linked to the genetic expression of the enzymes and regulatory proteins involved. A major achievement was made in 2016 when the complete salmon genome was released after sequencing three billions of DNA bases making up the salmon's 29 chromosomes. Mapping the genome also revealed how salmon strains and the salmonidae family may have evolved.

This new insight paved the way for efficient measurement of the level of expression of all genes in a tissue or blood sample from salmon. In addition, measurements of thousands of biomolecules and metabolites in the same samples can be fed into the model. Based on the data, a dynamic model that respond to variations in feeding, genetic background and other parameters will be constructed.

The knowledgebase in terms of the data and the model, will enable new analysis of already known aspects of the salmon's biology, discover knowledge gaps, further acquiring and incorporating new data, and there by develop and improve the model. The goal is that eventually this will be a tool used by the aquaculture industry to test out variants of salmon strains, feed and environment in a simulation, thereby foreseeing eventual challenges and problems before they occur in production. Hence, the title "from reactive to pre-emptive".


Mathematical models make it easier

The researcher view the salmon as a biological system built up of a set of components that rely on each other. To understand variation in a given phenomenon, such as body growth, the potential reactions and processes in the different organs contributing to the phenomenon are combined in a mathematical model that fits with the experimental measurements that can be sampled from salmon.

The benefit of describing physiological processes by mathematical models and run simulations is partly that the researcher can reveal new knowledge, and partly that wrong hypothesis' can be abandon before being tested in experiments. The researcher can therefore quickly select the feed mixtures that most likely will succeed, and then test these in actual feeding experiments.

In DigiSal the researcher especially study metabolism and how this is coupled to genes. They can measure what the salmon eats, how the feed is ingested and converted down to molecular level.

The mathematical model will be encoded with standardized nomenclature of the salmon's biochemical reactions, enzymes, reaction parameters, and molecules involved. The standardization allows automatic coupling of already established biochemical databases and datasets form other experiments.


The project gathers researchers that do mathematics, data analysis, informatics, sensor technology, genomics and experimental biology.

As so many disciplines and partners are involved, the project management emphasizes that the different experts should develop understanding of each others research areas and encourages the team to see possibilities and limitations within the project.

Most of the researchers are located at NMBU, Ås, but several of the project partners are located in other parts of Norway or abroad. The project partners will gather physically from time to time, but usually meetings and contact will be by Skype.

Responsible Research and Innovation

The project will emphasis the dialogue with lay people, researchers within and outside the project, industrial partners and representatives for the authorities. During the project seminars aimed at lay people discussing the use of systems biology for more sustainable food production, possibilities for industry development, and potential impacts of new technology on the consumer, will be arranged.

The project will also make data and models available and usable by a web-platform, integrated with a resource base of the salmon genome.


When the mathematical models are in place, the fish farmers will get recommendations about the feed mixture of their specific salmon strain. In the future, the fish farmers might get custom advice on dosing of the feed, incorporating weather and temperature data and forecasts, for optimal feeding.

For companies that develop new feed variants, the mathematical models will be a tool to select the best ingredients, resulting in shorter time from research to market with less failing animal experiments and lower costs.

For companies that breed new salmon strains, the model will enable them to speed up the process of selecting suitable fishes for further development and breeding, as well as quality control, surveillance and maintenance of their product,

Following the project and an increased need for monitoring and data acquisition, one could envisage development of devices and sensors for a future marked in aquaculture.

Watch presentation of the project

At the Digital Life 2020 conference postdoctoral fellow Ove Øyås talked about the project.
Watch recording of his talk.

Latest news from the project