PhD scholarship in interactions between fish microbiomes and health and welfare in aquaculture - DTU Aqua

Are you interested in exploring the interactions between early life environment, mucosal microbiomes, and life-long health and welfare in an important aquaculture fish species, rainbow trout? Are you comfortable both with a pipet on hand in the lab and getting out and working in collaboration with the aquaculture industry? Here is an opportunity for you! At DTU’s National Institute of Aquatic resources, we offer a 3-year PhD position with a focus on interactions between fish microbiomes and health and welfare in recirculating aquaculture systems (RAS). You will be employed in the Section for Aquaculture, located at our campus in Hirtshals in the beautiful Northern part of Denmark. 

The section is a vibrant international group that holds a strong expertise in the different aspects of aquaculture (e.g., farming technologies, water quality, fish physiology and nutrition, aquaculture microbiology), providing a scientifically stimulating multidisciplinary and multicultural environment. 

The microbiome is an essential contributor to animal health and welfare through participating in the vital physiological processes and guiding host development. The positive connection between diverse microbiome and animal health and welfare has been found in the terrestrial farmed animals, while many knowledge gaps remain in the aquatic farming environment due to diverse range of farmed species, rearing systems, and husbandry practices. This Ph.D. position aims to gain new knowledge on fish microbiome-health & welfare dynamics, the development, stability, and resilience of microbiomes and performance and robustness of fish with different microbiome profiles.

• Responsibilities and qualifications
• Your focus will be to examine the mucosal microbial communities and health and welfare indicators in rainbow trout at different life-stages in an aquaculture environment. 

Your responsibilities are expected to include:

• Designing and conducting fish experiments in aquaculture facilities
• Collecting biological samples and observational data
• Sample analysis in the laboratory using state-of-art molecular microbiology techniques and fish health and welfare analysis 
• Sequencing data analysis (bioinformatics)
• Scientific dissemination of results
• Completing the required PhD school courses and conducting an external research stay
• Teaching and supervision of MSc students

Desired Qualifications And Skills:

• Curiosity and high motivation for research
• A relevant background in microbiology, molecular biology, animal physiology, or a related field
• Experience in chemical, microbiological, and/or molecular laboratory work
• Experience in experimental work with fish and/or aquaculture systems
• Accuracy and patience for laboratory and experimental work
• Interest towards statistics and bioinformatics
• Strong written and oral communication skills in English
• Ability to work both independently and as a part of a team.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment 
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education. 

Assessment
The assessment of the applicants will be made by Senior Researcher Sanni-Leea Aalto, Senior Researcher Manuel Gesto, and Head of Section Per Bovbjerg Pedersen.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

• Salary and appointment terms
• The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. 

The period of employment is 3 years. Expected starting date is 1st of January 2026 (or according to mutual agreement)

• You can read more about career paths at DTU here.
• Further information Further information may be obtained from Senior Researcher Sanni-Leea Aalto, e-mail: sheaa@aqua.dtu.dk 
• You can read more about Section for Aquaculture at https://www.aqua.dtu.dk/english/about/organization/scientific-sections/section-for-aquaculture

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU. 

• Application procedure 
• Your complete online application must be submitted no later than 30 September 2025 (23:59 Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae 
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale

You may apply prior to ob­tai­ning your master's degree but cannot begin before having received it. 

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

About DTU Aqua
DTU Aqua – National Institute of Aquatic Resources – works for well-functioning oceans, rivers, and lakes where biodiversity can thrive. Our research, advisory service, and education contribute to the development of a sustainable blue bioeconomy, robust aquatic ecosystems, and reduced effects of climate change. We have a large national and international network and cooperate with research partners, public authorities, industry, and NGOs. We have state-of-the-art research facilities and Denmark’s only ocean- and arctic-going research vessel. The Institute has 360 employees, one-half being scientific staff, including about 50 PhD students. More than 35 nationalities are represented at the Institute, and we support an equal gender distribution. We are located in Lyngby, Hirtshals, Nykøbing Mors, and Silkeborg and have regular activities in Greenland. Learn more on aqua.dtu.dk

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.