Department of Biology, Marine Biological Section invites applicants for a PhD fellowship in bacteriophage-pathogen interactions and the potential of using phages to control fish pathogenic bacteria in the production of fish in aquaculture. The project is part of the research project “Cure4Aqua”, which is a Horizon Europe project financed by the EU.

Start date is 1 May 2023 or as soon as possible thereafter.

The project

Diseases at the larval and fry stages constitute a major bottleneck and cause economic losses to the aquaculture industry, a problem that has increased dramatically with the intensification of aquaculture production. The project focuses on the important fish pathogens, Flavobacterium psychrophilum and a group of marine Vibrio pathogens, which are causing diseases in Rainow trout and European Sea Bass, respectively. Vaccines are not effective at the larval and fry stages, and antibiotics are needed to control these pathogens. Antibiotic treatment is associated with serious concerns about the development of bacterial antibiotic resistance and its potential transfer to human pathogenic bacteria. In this project we aim at developing alternative environment-friendly approaches based on natural microbial warfare, using bacteriophages (phages).

The PhD project will focus on key elements of phage-based applications in these specific groups of pathogens, including 1) phage-pathogen interactions and diversity, 2) mechanisms and implications of phage resistance, 3) phage production, stability and delivery, 5) phage efficiency in reducing pathogen load and fish mortality. This includes isolation and characterization of broad host-range phages from aquaculture environments, investigations of genomics, evolution, host range and lytic potential of the isolated phages, and optimization of phage production and delivery. Further, phages will be applied to live feed and fish fry in both lab- and farm-scale experiments with Rainbow trout and  Sea bass. The work will entail a combination of microbiological analyses (phage Isolation, and cutting-edge molecular and bioinformatic approaches (e.g. Real-Time PCR, genomic sequencing, microbiome analysis), in association with laboratory experiments.

Who are we looking for?

We are looking for an enthusiastic and ambitious candidate within the fields of microbiology/molecular biology/aquatic biology and a strong interest in bacteriophage biology and phage-host interactions. Documented knowledge and experience on bacteriophage biology, use of phage in pathogen control and bioinformatics is an advantage. The position is open to both Danish and international applicants, and good English language skills will be required. The main criterion for selection will be the research potential of the applicant.

Our group and research- and what do we offer?

The successful candidate will become an integrated part of the research group of Professor Mathias Middelboe. We offer creative and stimulating working conditions in dynamic and international research environment, with recently renovated labotratory facilities and state of the art equipment for phage research.The group works with many aspects of marine microbial ecology, including deep sea microbiology and phage therapy, and bacteriophage genomics, ecology and potential use in disease control are key research areas in the group. We have long-term experience with phage-pathogen research, primarily focusing on phage-host interactions in Flavobateria and Vibrio pathogens. The project is therefore a continuation of previous projects on the topic. The Cure4Aqua project is carried out as a collaboration between >25 partner institutions, and part of PhD work will be in collaboration with Swansea University, UK, The Hellenic Center For Marine Research, Greece and the Danish Technical University, and in close collaboration with other Cure4Aqua PhD students and post docs from these institutions. The project will be carried out at the Middelboe Lab at Marine Biological Section, located in Helsingør, 45 km north of Copenhagen. However, research visits and experimental work at partner institutions are also part of the PhD program The section is part of the Department of Biology, Faculty of SCIENCE, University of Copenhagen.

Principal supervisor is Professor Mathias Middelboe, Marine Biological Section, Department of Biology. E-mail: Phone: (+45 41178798).

The PhD programme

The position is a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.Option A: A three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. aquatic microbiology, phage biology. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

  • Carry through an independent research project under supervision
  • Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
  • Participate in active research environments, including a stay at another research institution, preferably abroad
  • Teaching and knowledge dissemination activities
  • Write scientific papers aimed at high-impact journals
  • Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

  • Professional qualifications relevant to the PhD project
  • Relevant publications
  • Relevant work experience
  • Other relevant professional activities
  • Curious mind-set with a strong interest in microbiology and bacteriophages
  • Good language skills


Application and Assessment Procedure

 Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include

  1. Motivated letter of application (max. one page)
  2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
  3. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
  4. Publication list (if possible)

Application deadline:

The deadline for applications is 1 February 2023, 23:59 GMT +1.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at

Interviews with selected candidates are expected to be held in weeks 7 and 8.

For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website:

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position. 


Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.


Mathias Middelboe



Application deadline: 01-02-2023

Employment start: 01-05-2023

Department/Location: Department of Biology

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