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Prosjektnummer: 901436
Status: Pågår
Startdato: 01.11.2017
Sluttdato: 31.12.2021

Use of microbiome-genome co-optimisation to improve gut health and growth in farmed salmon (HoloFish)

Aquaculture provides >50 per cent of all consumed fish, is the fastest growing food-producing sector worldwide, and is predicted to grow by ≥5 per cent annually in years to come. The salmon industry’s rapid growth presents an urgent need for a greener transition towards economically and environmentally sustainable production. Yet, as with many types of farmed animals, salmon aquaculture faces challenges such as regular disease outbreaks, inefficient feed conversion and losses due to unpredictable variation in fish size at harvest.
Improving feed utilisation/efficiency presents a major potential for salmon farmers; as nearly 60 per cent of salmon production costs come from fish feed, there is a demand for new solutions to reduce such costs. In recent years, the aquaculture industry has endeavoured to develop more sustainable and higher quality fish products. These efforts included (1) promoting the use of plant-based, cost-effective fish feed, (2) focusing on functions provided by the gut-microbiota, and (3) selective breeding to achieve higher yield and improved fish health.
Researchers have conventionally explored whether such variation can be explained by variation in the salmon’s own genes, but often with limited success. Attention has recently turned towards an alternate explanation, the fishes’ gut microbiome. Rapidly accumulating evidence suggests that many salmon host-associated microorganisms are not passive passengers, but active crew, who can affect and even condition growth and health parameters in salmon. Numerous studies have attempted to understand the relationships between gut microbes and salmon phenotypes, but it is becoming clear that growth or disease resistance cannot simply be explained by the effect of the microbes alone. Might there be a solution to these challenges? The project proposes the answer is yes, and that it lies within their ‘hologenome’.
Hologenomic theory offers potential to better understand and improve feed conversion in farmed fish. Specifically, hologenomic theory argues that the genomes of host organisms and their associated microbial communities are subjected to co-evolutionary forces and constitute a larger super-organism, the ‘holobiont’. Thus the host organism and its microbiome should be studied as a single unit, the hologenome. Intriguingly, recent scientific work indicates that changes in growth and health traits of farmed fish result from the interplay among the host genotypes, host physiology, host gut microbiota, as well as feed and environmental factors. Therefore, to best manipulate such traits, one must consider the genome and microbiome together, but such attempt has never been made in an aquaculture context.
This project present a hologenomic approach to address the prioritised area ‘Reduction of losses and robust fish’ according to FHF’s action plan, and specifically relates to research for improving and maintaining proper gut health in salmonids.
Main objective
To provide new knowledge for improving gut-health in salmonids, in order to identify how the growth rate of farmed salmon is affected by the interacting effects of the feed composition, gut–microbiota and the salmon host genome.
1. To sample tissue, gut content and gut-mucosal samples from sea-farmed salmon that are fed on three commercial diets, and within each treatment, exhibit variable sizes at harvest age.
2. To use this data to characterize the genome, epigenome and transcriptome for each individual salmon, as well as the metagenomes, transcriptomes and metabolomes of their gut contents.
3. To apply association mapping to these parameters within a hologenomic framework in order to decipher the link between salmon genomes and their gut microbiota composition and activity, how this relates to dietary treatment, and how these in turn affect growth, feed conversion, health and muscle fatty acid profile.
4. To implement hologenomic insights about host-microbiome interactions into current breeding and feeding regimes. 
5. To optimize the match between the salmon’s genetic background and it's diet, so as to optimize gut-health and growth output.
Expected project impact
Holistic insights on interactions among feed and a salmon’s genome and gut microbiome will lead to new actions that will improve gut health and conversion of feed to fish biomass. Anticipated principal outputs are to:
1. Decipher the genomic and/or epigenomic mechanisms that shape microbiome community structure in farmed Atlantic salmon.
2. Identify microbiomes that optimise health and growth/feed conversion in these populations.
3. Develop biomarkers for selective breeding of salmon genotypes that effectively maintain gut-microbiota that optimise health and growth.
4. Intelligently match commercially available diets with the hologenotype of the farmed salmon broodstock, to optimise health and growth.
5. Develop new methods and tools to associate genomic background with gut microbial community of interest to other breeding systems in aquatic and terrestrial plants and animals.
Project design and implementation
An international consortium of complementary resources and expertise will conduct this research through four work
packages (WPs):
WP 1: Growth and feed experiments and sampling
There will be sampled several tissues and gut contents from 360 adult Atlantic salmon that have been raised under three different diets in commercial sized cages (120 fish per diet).
WP 2: Molecular analyses
In this work package there will be generated multiple levels of molecular data for the salmon hosts: i) genome, ii) gene expression profiles, iii) epigenome profile, and iv) muscle fatty acid profile. Similarly, for the salmon gut microbiome there will be generated data for: i) microbial genomes, ii) microbial gene expression profile, and iii) metabolome of the gut.
WP 3: Data analyses
Data from WP 2 will be analyzed using first existing protocols for describing molecular differences in host and gut-microbial composition/function among size groups and commercial diets. Second, there will explored whether correlations exist between salmon genome and/or epigenome and/or transcriptome, with microbial genome and/or genes and/or transcriptome.
WP 4: Validation experiments
New biomarkers for monitoring fish health will be developed based results in work package 3, and tested for application in commercial production by Lerøy. These new biomarkers will provide a tool for helping aquacultural firms improve fish health as well as their productivity.
Project organization
• The project will be anchored at the Norwegian University of Science and Technology (NTNU) in Trondheim with responsible project leader Prof. Tom Gilbert.
• Lerøy will be in charge of growing fish on different diets and organize sampling of adult fish and validation experiments.
• NIFES will generate data for salmon fatty acid profiles.
• NTNU and University of Copenhagen (UCPH) will generate molecular data from salmon samples and analyze the data.
• All partners will work closely with the established steering committee throughout the project to assure an industrial relevance and focus of project activities. 

Preliminary results 
Morten. T. Limborg, Antton Alberdi, Miyako Kodama, M​ichael​​ Roggenbuck, Karsten Kristiansen, and M.​ Thomas P. Gilbert, ‘Applied Hologenomics: Feasibility and Potential in Aquaculture’​, Trends in Biotechnology 36/​3, 1 March 2018, 252​64. For an abstract and ordering details, see the CellPress website​ at
Dissemination of project results
The project group will implement a dissemination strategy designed to maximize timely sharing and publication of research results for the benefit of industrial end-users and other stakeholders.
During the project period, preliminary results will be presented on internal steering committee meetings, conferences and seminars, both orally and as posters at e.g. AQUA 2018 (Montpellier, France, 2018) and Aquaculture Europe 2019 (arranged by European Aquaculture Society, Berlin, Germany, 2019). The project group will also contribute with its findings to relevant national events such as FHF's yearly conferences.

Popular scientific articles will be published in both international (e.g. Aquaculture Magazine) and national (e.g. Ilaks.no intrafish.no and/or kyst.no) magazines and newspapers. Popular summaries of scientific publications will be further communicated through press releases and newsletters in collaboration with the in-house communication units at NTNU and NIFES, as well as through a dedicated blog hosted by NTNU.

At least five main manuscripts are expected from the core activities.