Back to search

HAVBRUK2-Stort program for havbruksforskning

ERA-NET: BlueBio - Improving aquaculture sustainability by modulating the feed-microbiome-host axis in Fish

Awarded: NOK 5.8 mill.

Human population growth is driving a rise in production for food such as farmed fish, which necessitates more efficient and sustainable practices. One promising route to achieve this, is to unravel the connection between the feed a fish eats, their bodily function and the microbes in their gut, not only to optimize nutrition but also to improve their health and welfare. Within the ImprovAFish project, we will collectively study Norwegian salmon, its diet and all its microbes as one unit (the holobiont), using a strategy otherwise known as holo-omics. This approach, enabled by recent biotechnological developments, can improve our understanding of how salmon digest their feed and sustain their growth. ImprovAFish combines novel prebiotic feed ingredients, fish experiments and holo-omics to jointly analyze salmon, their feed and their microbes. The outcome will be optimization of feeding strategies customized to specific types of salmon, to ultimately improve their growth and production whilst reducing their carbon footprint. Together with our project partners, a 5-month temporal feeding trial in land tanks was successfully conducted during the first year of the project (2020). From this trial we generated liver, gut epithelial and gut content samples from 120 fish divided across four different feeds (control and three prebiotic variations), 3 time periods (both fresh and salt water), and 3 replicate tanks. In addition, key performance indices were measured regarding growth metrics, welfare indicators and organ integrity. From samples collected we generated “holo-omic” (DNA, RNA, protein and metabolites) datasets, however our analysis determined that the next generation functional feed ingredient used in this experiment had limited impact towards modulating the microbiome and did not improve growth in salmon. Nonetheless, to support the analyses that made these determinations, we developed two new resources: the Salmon microbiome genome (SMG) atlas, which is a catalogue of microbial genomes that have been recovered from culture and metagenomic technologies. Selected bacteria from this atlas, which were detected in our in the aforementioned in vivo fish trials, have been metabolically characterized in detail and several species show beneficial properties, converting dietary compounds (such as carbohydrates and amino acids) into vitamins and organic acids. Secondly, we built a bioinformatic framework called OmniCorr, which explores correlations between different omics datasets. Using OmniCorr, we identified modules of co-expression originating from the host and microbiome and future work will assess whether there exists any underlying biology that depicts putative functional coupling that could be exploited. We envisage these resources will not only serve the interests of this project, but also act as resources for the greater scientific community as well as industry. Additionally, in the fall of 2021 we held a 3-month trial in sea cages to generate samples for a genome-wide association study (GWAS) aiming at identifying host genetic traits in salmon broodstock that are associated with specific microbiome compositions under two different dietary conditions. It is expected that data analysis from these samples, which is currently ongoing, will reveal if reproducible biological connections exist between host genetic variance and the types of microbes that inhabit the salmon gut. Such knowledge could be exploited by fish breeders to select for fish with inherent beneficial bacteria and/or feed manufacturers to include ingredients that match the metabolic capabilities of heritable microbiota. In parallel to our scientific experiments, we have engaged in exercises to identify relevant stakeholders to interview in order to understand the potential impacts of ImprovAFish, and how alterations in salmon feed are socially, ethically and culturally relevant. Findings from the interviews were summarized around the following four central topics, sustainability, efficiency, ethics and responsibility that were deemed high impact with regards to feed alterations. Overall, ImprovAFish will create opportunities for aquaculture to facilitate optimization of improved and sustainable feeding strategies that are customized, with an emphasis on socially responsible outcomes facilitated by a dedicated Responsible Research and Innovation process.

Actual outcomes and impacts of results arising from ImprovAFish are embedded in increased awareness of the exploitation potential of microbiomes to support growth in aquaculture. ImprovAFish has generated outcomes and impacts at the following levels: • We have launched the Salmon Microbiome Genome Atlas (SMGA), which consolidated a genomic catalog from multiple sources using metagenomics, single cell genomics, culturomics and long read technology that ensures high quality circular genomes with encoded 16S rRNA gene operons. The SMGA consists of 211 high-quality bacterial genomes, and its application has discovered interactions between uncharacterized and as-yet uncultured salmon microbiota at different development stages. We have for the first time demonstrated in vivo characterization of key populations in the salmon gut, with their ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects being validated via in vitro cultivation and metabolomics. • Applied microbiome technologies to fish feeding trials has holistically assessed the novel prebiotic feed ingredient beta-mannan, and if various microbial metabolic activities are connected to actual phenotypic outcomes in the host fish. While we have not finalized the necessary analysis that is required to fulfil this impact, preliminary indications are the beta-mannan does NOT have a prebiotic effect in the GI tract of salmon. • Via RRI activities the project has explored how feed producers for aquaculture can achieve a social license to operate. Through a methodological triangulation, with stakeholder interviews, a project workshop, and a documentary analysis of annual reports from relevant businesses, the project outcomes identified 8 salient issues: Sustainability; Circularity; Power and governance; What consumers desire; Feed efficiency; Uncertainties; Untapped resources; Regulations, certifications and standards. What these issues entail is specified in a published white paper, together with suggestions to the research policy on feed for aquaculture. • It has created versatile methodological resources/toolkits, which will be published in scientific papers, and which are reproducible for current industrial partners as well as future salmon industrial/academic studies that seek to examine alternative dietary and/or environmental conditions to improve animal growth and health. For this impact we have generated two unexpected knowledge resources, the SMGA and OmniCorr.

As the human population surges towards 10 billion, the production and consumption of aquaculture products such as fish is expanding. Therefore, efficient and environmentally sustainable practices are required to ensure long-term food security. To solve these challenges, attractive solutions include developing new feed ingredients and better broodstock genetics to improve fish production and welfare. Intriguingly, it has been shown that both feed and host genetics can modulate the gut microbiome of animals and thus influence its integral connection to host phenotype. The ambitious aim of ImprovAFish is to decipher the intimate functional coupling along the feed-microbiome- host axis in an applied context, with the emphasis on a promising ‘next generation’ functional feed ingredient (beta-mannan) that is known to promote beneficial microbiota in livestock and has shown promising preliminary results in fish. Our approach is to jointly analyze how diet affects the metabolic function of the host and its microbiome as a single unit of action, using a novel and powerful framework called “holo-omics”. This entails monitoring how changes in enzymes and metabolites produced by microbiota correlates with uptake and metabolism of nutrients in the gut and liver of the fish. By doing this across life stages, different feeds and with recordings of key performance indices, we aim to identify exploitable interactions between specific feed components and microbiome functions that can be used to improve fish phenotype. In addition, associations between broodstock genetic variation, microbiome composition and diet will be determined, which will facilitate selection for fish with preferred gut microbiota. Ultimately ImprovAFish will facilitate optimization of improved and sustainable feeding strategies that are specifically tailored to host genetics (or vice versa), with an emphasis on socially responsible outcomes facilitated by a dedicated Responsible Research and Innovation process.

Publications from Cristin

No publications found

No publications found

Funding scheme:

HAVBRUK2-Stort program for havbruksforskning

Thematic Areas and Topics

Politikk- og forvaltningsområderSkog, landbruk og matDelportefølje InternasjonaliseringLTP3 Samfunnssikkerhet og beredskapBioteknologiLandbruksbioteknologiUtviklingsarbeidDelportefølje KvalitetResponsible Research & InnovationRRI Utviklings- og prosessorienteringFNs BærekraftsmålMål 2 Utrydde sultBioteknologiInternasjonaliseringInternasjonalt prosjektsamarbeidBioteknologiMarin bioteknologiInternasjonaliseringPortefølje Muliggjørende teknologierInternasjonaliseringInternasjonalt samarbeid om utlysningHavbrukFôr og ernæringLTP3 Fagmiljøer og talenterAnvendt forskningLTP3 Rettede internasjonaliseringstiltakMarinMarin bioteknologiLTP3 Høy kvalitet og tilgjengelighetDelportefølje Et velfungerende forskningssystemLTP3 Samfunnsikkerhet, sårbarhet og konfliktBransjer og næringerFiskeri og havbrukHavbrukFiskehelse og velferdMarinMatGlobal matsikkerhetFNs BærekraftsmålLTP3 Nano-, bioteknologi og teknologikonvergensPolitikk- og forvaltningsområderLTP3 Muliggjørende og industrielle teknologierLTP3 Et kunnskapsintensivt næringsliv i hele landetBioøkonomiØvrig bioøkonomiPortefølje ForskningssystemetBioøkonomiMatKlimarelevant forskningPortefølje Mat og bioressurserBransjer og næringerPolitikk- og forvaltningsområderFiskeri og kystLTP3 Hav og kystCo-Funded/ERA-NETResponsible Research & InnovationCo-Funded/ERA-NETERA-NET Cofund H2020HavbrukLTP3 Bioøkonomi og forvaltningLTP3 Klima, miljø og energiLTP3 Marine bioressurser og havforvaltningLTP3 Styrket konkurransekraft og innovasjonsevneMarinHavbrukMatMat - Blå sektor