PhD students

Background of the project
The aquaculture microbiome balance is crucial for the health status of the system, such that dysbiosis has been reported when a stressor, such as a pathogen, is introduced. Current farmed fish diagnostics methods consist in infection event monitoring and imply histopathology, culture isolation, and targeted molecular diagnostics for the suspected pathogen. However, this approach comes with drawbacks: action is only taken after manifestation of clinical signs or increased mortality, and standard diagnostics are targeted towards known pathogens, which impairs new pathogen discovery, especially when the microorganisms are unculturable.

About the project
My PhD project aims to develop a rapid, untargeted NGS-mediated workflow for early detection of declining health conditions and microbial disease for farmed animals in aquaculture, by exploiting the microbiome as an indicator for the state of the system. First, I will implement a microbiome sequencing protocol with Oxford Nanopore Technology from various aquaculture-relevant samples, both environmental (eDNA) and host-associated. Then, I will test the protocol in stress-induced conditions (pathogen, organic waste) in experimental RAS facilities, to detect possible changes in the healthy microbiome associated with fish health. The protocol will then be translated to detect distress-correlated dysbiosis in industry samples. Finally, I will apply metagenomics sequencing for pathogen discovery for a salmonid skin disease, whose unculturable disease-causing agent is still unknown.

Perspectives
My project aims to exploit aquaculture-related microbiome sequencing to integrate current diagnostics with a non-lethal, fast and untargeted community surveillance method. If successful, the outcome of my PhD could represent the first steps towards the development of a novel indicator of fish health, such as microbiome risk scores for disease prediction. Early detection of distress could favour preventive strategies to minimize the impact on aquaculture production.

Supervisors
Argelia Cuenca and Lone Madsen, DTU Aqua & Thomas Nordahl Petersen, National Food Institute

Background of the project
The immune system in animals is a multi-faceted defense mechanism against pathogens. In vertebrates, the immune system operates through both innate and adaptive mechanisms, the latter being capable of generating immunological memory. Traditionally, invertebrates, such as shrimp, have been understood to possess only innate immune systems, devoid of any capacity for immune memory. This paradigm is being challenged as more research suggests invertebrates demonstrating a form of immunological memory, albeit not antibody-based. Understanding this could have a broad impact on industries like aquaculture, which often grapple with viral diseases that threaten shrimp populations.

About the project
This PhD project aims to explore the role of circular viral DNA (cvDNA) in the immune response mechanism of shrimps against invading viruses. Utilizing Penaeus vannamei (Pacific whiteleg shrimp) as a model organism, the project will investigate whether cvDNA molecules are produced during viral infections and if these molecules serve as templates for RNAi-induced antiviral immune response. The project aims to address the biological aspects of cvDNA as well as its potential for conferring viral resistance and longevity of immunity. Methodologically, the study will employ a combination of molecular techniques, sequencing, and bioinformatics analysis to examine  cvDNA and its implications.

Perspectives
The implications of this research extend beyond shrimp aquaculture. If shrimp do possess a form of immune memory mediated by cvDNA, this could revolutionize our understanding of invertebrate immunity and even have repercussions for vertebrate immune systems. Moreover, it could open up new avenues for combating viral diseases in commercial aquaculture. The robust nature of cvDNA may offer innovative methods for studying virus-host interactions, both in contemporary and historical contexts. This has implications not only for animal husbandry but also for broader public health policies, especially considering the emerging evidence that vertebrates may utilize similar pathways.

Supervisors
Niels Lorenzen and Dagoberto Andres Sepulveda Araneda, DTU Aqua & Morten Schiøtt, DTU Bioengineering

Background of the project
The immune system in animals is a multi-faceted defense mechanism against pathogens. In vertebrates, the immune system operates through both innate and adaptive mechanisms, the latter being capable of generating immunological memory. Traditionally, invertebrates, such as shrimp, have been understood to possess only innate immune systems, devoid of any capacity for immune memory. This paradigm is being challenged as more research suggests invertebrates demonstrating a form of immunological memory, albeit not antibody-based. Understanding this could have a broad impact on industries like aquaculture, which often grapple with viral diseases that threaten shrimp populations.

About the project
This PhD project aims to explore the role of circular viral DNA (cvDNA) in the immune response mechanism of shrimps against invading viruses. Utilizing Penaeus vannamei (Pacific whiteleg shrimp) as a model organism, the project will investigate whether cvDNA molecules are produced during viral infections and if these molecules serve as templates for RNAi-induced antiviral immune response. The project aims to address the biological aspects of cvDNA as well as its potential for conferring viral resistance and longevity of immunity. Methodologically, the study will employ a combination of molecular techniques, sequencing, and bioinformatics analysis to examine  cvDNA and its implications.

Perspectives
The implications of this research extend beyond shrimp aquaculture. If shrimp do possess a form of immune memory mediated by cvDNA, this could revolutionize our understanding of invertebrate immunity and even have repercussions for vertebrate immune systems. Moreover, it could open up new avenues for combating viral diseases in commercial aquaculture. The robust nature of cvDNA may offer innovative methods for studying virus-host interactions, both in contemporary and historical contexts. This has implications not only for animal husbandry but also for broader public health policies, especially considering the emerging evidence that vertebrates may utilize similar pathways.

Supervisors
Niels Lorenzen and Dagoberto Andres Sepulveda Araneda, DTU Aqua & Morten Schiøtt, DTU Bioengineering

Background of project
Rearing fish at high densities increases the risk of spreading pathogenic viruses and bacteria, particularly in larvae and fry. An important fish pathogen in aquaculture is Flavobacterium psychrophilum, the etiological agent of Rainbow Trout Fry Syndrome (RTFS), that causes significant economic losses in hatcheries worldwide. Cases of reduced susceptibility to antibiotics underline the need for alternative and more sustainable methods for the treatment of this bacterial infection, such as bacteriophage-based therapy. Bacteriophages (also called phages) are host-specific viruses of bacteria. Their use has recently demonstrated promising results in controlling various infectious fish diseases. However, further development is needed for the commercialization of this solution as a novel prophylactic product.

About the project
Besides investigating the efficiency of phage administration in controlling RTFS by performing in vivo experimental infection trials, this PhD project will specifically target rainbow trout (Oncorhynchus mykiss) health status and host-pathogen interactions. In particular, the host immune response to phages will be assessed through gene expression analyses using qPCR, while the effects on fish microbiota and tissues development will be evaluated through sequencing and histological techniques, respectively. Once considered as safe, the most efficient phage preparations will be administered to fish/tanks using different strategies (feed pellets, liquid solution, coating on elements of the filtration system of tanks) to establish the best delivery method, before testing this disease control strategy under farming conditions.

Perspectives
The final goal of this PhD project is to perform an efficiency and risk assessment of the phage-based solutions. This represents one of the tasks of a larger IFD research project, AQUAPHAGE whose final aim is to develop bacteriophage-based products that target specifically the bacterium F. psychrophilum, and to bring these solutions to a commercially viable stage. This new sustainable and innovative method can increase production efficiency and reduce the environmental burden of aquaculture. 

Supervisors
Lone Madsen & Valentia Donati, DTU Aqua

Background of the project
Aquaculture is the most sustainable form of animal husbandry in terms of environmental impact, but infectious diseases cause significant losses, often requiring antibiotics. Lost production as well as use of antibiotics compromise both financial and environmental sustainability of aquaculture. The key to overcoming these problems is improved disease prophylaxis, with vaccination being one of the most effective tools. While injection vaccination is well established for larger-sized fish, early vaccination of smaller fish is less developed due to the lack of efficient vaccines delivered by mucosal routes. The mechanisms of immune activation and protection remain to be fully understood.

About the project
The project aims to develop and test formulation strategies for mucosal delivery of recombinant viral vaccines based on DNA and/or recombinant proteins in rainbow trout (Oncorhynchus mykiss), targeting diseases that infect early life stages. First, I will optimize the vaccine formulation by incorporating mucosal adjuvants and explore different delivery methods, including inactivated transformed bacterial cells. Next, I will test vaccination strategies, focusing on dose, delivery, and adjuvant aspects under laboratory conditions. Finally, I will evaluate the protective immunity in vaccinated fish through infection trials and identify immune response elements correlating with protection, providing insights into immune mechanisms and ensuring long-term vaccine efficacy.

Perspectives
Optimized mucosal vaccines that enhance uptake and stimulate both mucosal and systemic immune responses could address disease problems in small-sized fish. These vaccines would be easier to administer, reduce labor costs, and ultimately contribute to the overall health and welfare of fish population. This approach will not only improve aquaculture productivity and sustainability but also offer valuable insights into the mechanisms of fish mucosal immunity, thus, contributing to the broader field of immunology and vaccine development.

Supervisors
Niels Lorenzen & Dagoberto Andres Sepulveda Araneda, DTU Aqua

Background
Danish aquaculture is a relatively small but stable food production sector, with a strong emphasis on sustainability. However, disease outbreaks pose a significant threat to productivity and profitability. While economic evaluations of aquaculture diseases exist in other regions, there is limited research specifically addressing the economic impact of diseases in Denmark’s aquaculture sector.

About the Project
The first part of this project aims to assess the economic burden of the fish disease IHN in Danish aquaculture, with the potential to expand its scope to other diseases in later project segments. A combination of economic evaluation methods, including cost-benefit analysis, modeling, and case studies, will be applied. The research will utilize a range of data sources, including industry reports, farm-level data, and government statistics, to provide a comprehensive analysis. Additionally, this work is being conducted as part of the EUPAHW partnership, which facilitates collaboration on animal health and welfare issues at a broader European level.

Perspectives
The findings of this research are expected to support key stakeholders—such as farm owners, managers, and policymakers—in making informed decisions regarding disease management. By quantifying the economic impact, the study can contribute to more effective planning for disease surveillance, eradication, and control programs. However, a key challenge may arise if the results suggest increased investment in prevention and eradication efforts, as there could be resistance from those bearing the financial burden. Addressing these concerns through well-informed policy recommendations will be crucial for the practical application of the research outcomes.

Supervisors
Britt Bang Jensen, DTU Aqua & Henk Hogeveen, Wageningen University & Søren Østergaard, Aarhus University