This article was featured in Eurofish Magazine 1 2026.
Researchers at the Department of Biology, University of Copenhagen, are driving a project that seeks to reduce antibiotic use in the rainbow trout farming industry with multiple potential benefits.
As global demand for seafood continues to rise, aquaculture has become central to supplying high-quality protein. At the same time, bacterial diseases remain one of the main constraints on production, and antibiotics are still widely used to manage outbreaks. This reliance has contributed to the spread of antibiotic resistant bacteria creating risks for animal health, human health, and the wider ecosystem. Recent scientific reviews suggest that antibiotic resistance now threatens the intensification of aquaculture unless alternative tools are developed.
Among the alternatives, bacteriophage therapy has attracted particular interest. Bacteriophages—viruses that infect bacteria—can be selected to kill specific pathogens without harming fish or disrupting the broader microbial community. A 2025 review of phage therapy in freshwater and marine aquaculture species highlights successful experimental applications against key fish pathogens in the genera Aeromonas, Vibrio, Edwardsiella, Streptococcus, and Flavobacterium, although most work has so far remained at laboratory or small-scale trial level. A complementary 2024 review focused on alternatives to antibiotics in aquaculture summarises why phages are so attractive in this context. Lytic phages, which infect bacteria and reproduce by taking over the host cell machinery killing the host and releasing phage particles that infect more bacterial cells, have narrow host ranges, and have not been associated with adverse effects on fish or the environment. They can be delivered in several ways—via water, feed, injection, or topical application—and maintain activity over a broad range of temperature, salinity, and other water quality conditions. Yet the review also stresses that farm-ready phage products should be strictly lytic (as opposed to lysogenic, where the phage reproduces by integrating its genome into the host chromosome), formulated in cocktails to limit resistance, tested for survival under real farming conditions, and produced at a cost farmers can bear. At the University of Copenhagen’s Department of Biology, Professor Mathias Middelboe heads a project, Aquaphage, launched with a clear goal of moving phage therapy from the laboratory to commercial applications for disease prevention in trout farming.
Targeting pathogens to boost yields in trout
Rainbow trout is one of the most important farmed fish in the European Union. Each year, more than 250,000 tonnes are produced, with an estimated value of around €660 million. The EU accounts for about 30% of global trout production, and Denmark alone produces roughly 12% of EU farmed trout, with national production growing by about 20% between 2012 and 2019.
A particular challenge arises in early life stages. Trout eggs, larvae, and fry are highly vulnerable to bacterial infections, yet they cannot easily be vaccinated, and treatment options are limited. As a result, antibiotics are often used when outbreaks occur, especially in hatcheries and recirculating systems that rear young fish. This situation raises the risk of selecting for resistant pathogens and of transferring resistance genes to other bacteria in the production environment, feed chain, and surrounding waters.
Flavobacterium psychrophilum is a major cause of disease in these early life stages. Infection can lead to substantial mortality and lost production in salmonids. Experimental studies have already shown that specific phages can infect and control F. psychrophilum in vitro, and in some fish models, but there are still no licensed, standardised phage products targeting this pathogen for use on farms. This gap—between promising phage science and practical disease control tools—is precisely what Aquaphage aims to close.
Designing phage-based products from lab to farm
Aquaphage is coordinated from the Department of Biology (UCPH BIO) at the University of Copenhagen. The scientific work begins with the isolation and characterisation of bacteriophages that infect F. psychrophilum. At UCPH BIO, researchers identify strictly lytic phages, examine their host range, and assess their genomic safety to avoid any phages that might carry virulence or antibiotic resistance genes. Promising candidates are then combined into cocktails that can address the diversity of field strains while limiting the risk that bacteria will evolve resistance to any single phage. These phage combinations are first evaluated at laboratory scale, where researchers work to optimise dose, timing, and delivery routes. Immersion treatments can be effective for pathogens on skin and gills, whereas oral delivery via feed is more suitable for infections in the gut or systemic disease, provided that phages remain viable through feed processing and digestion. Aquaphage designs products specifically for trout hatcheries and recirculating systems, where phages are expected to be used as preventive tools rather than only as emergency treatments.
The Technical University of Denmark’s National Institute of Aquatic Resources (DTU Aqua) then tests phage performance in aquarium-scale experiments. Using reproducible infection models with F. psychrophilum, DTU Aqua quantifies how different product types influence pathogen load and fish performance in eggs, larvae, and juveniles. This stage is essential for translating laboratory results into realistic expectations of efficacy under farming conditions, including the influence of water quality, stocking density, and system design on phage dynamics. Scaling up phage production is caried out at the Danish Technological Institute (DTI) where experiments determine long-term phage survival in water and on coated feed to ensure both biological impact and acceptable production costs, particularly in recirculating aquaculture systems where phages can remain in circulation and contribute to prolonged protection. A distinctive feature of Aquaphage is its use of immobilised phages. DanAqua, a Danish producer of rainbow trout fry, hosts farm-scale trials, providing facilities where phage-based products can be assessed under commercial conditions and where feedback from end-users helps refine product profiles.
Building partnerships for a greener aquaculture sector
Aquaphage is designed not only as a biological research project, but also as an innovation effort that spans microbiology, engineering, economics, and regulation. The consortium brings together academic partners, public institutes, and private companies from Denmark, England, and Scotland. Alongside UCPH BIO and DTU Aqua, the University of Copenhagen’s Department of Food and Resource Economics (UCPH IFRO) assesses market potential and environmental impacts of the phage-based products, ensuring that economic analyses and life-cycle considerations inform development decisions. On the commercial side, Carus Animal Health provides expertise in product development and routes to market. Other partners providing technical knowhow include Fixed-Phage, KSK Aqua, and Aller Aqua, while DanAqua offers practical feedback related to cost and performance from testing on a commercial farm. By aiming to deliver phage-based products that can be used preventively as feed supplements or on biofilters in trout farms, the project seeks to reduce reliance on antibiotics and lower disease-related losses. If successful, the project will not only provide new tools against F. psychrophilum in rainbow trout but also offer a practical model for integrating phage therapy into routine aquaculture health management with benefits for fish welfare, producer profitability, and for attempts to curb antibiotic resistance in aquatic food production.
