Post doctoral research position in Bacteriophage-Pathogen Interactions

Post doc project in Bacteriophage-based pathogen control in trout aquaculture
Department of Biology
Faculty of SCIENCE
University of Copenhagen


Department of Biology, Marine Biological Section invites applicants for a Post doc position in bacteriophage-pathogen interactions and the potential of using phages to control Flavobacterium  pathogens in the production of raibow trout in aquaculture. The project is part of the research project “AQUAPHAGE”, which is project supported by the Innovation Fund Denmark (IFD).

Start date is 1 September 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, which are causing diseases in Rainow trout. 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 post doc 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. Further, phages will be applied to feed pellets and biofilters in both lab- and farm-scale experiments with Rainbow trout fry. 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. Moreover, the post doc will support the project coordinator in project management and internal communication, including communication and interactions with all project partners, reporting to IFD and the steering committee, organization of meetings and workshops, and co-supervision of PhD- and master students. 

Who are we looking for?

We are looking for an enthusiastic and ambitious candidate with a PhD degree in the fields of bacteriophage biology and general microbiology/molecular biology/aquatic biology and with experience in phage-based pathogen control and phage-host interactions. Documented experience in work with phage therapy applications 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 AQUAPAHGE project is carried out by a consortium of 9 partner institutions/private companies from Denmark and the UK, led by professor Middelboe. The work will be carried out in close collaboration with other post docs and PhD students and in this and related projects. 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 project. 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).

Terms of employment.
The eomployment will be full time and for 2 years and 9 months and it is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

Negotiation for salary supplement is possible.

The application, in English, must be submitted electronically by clicking APPLY NOW below.

We are looking for the following qualifications:

  • Professional qualifications (PhD degree) relevant to the project
  • Relevant publications
  • Relevant work experience
  • Other relevant professional activities
  • Curious mind-set with a strong expertise and track record in bacteriophages and general microbiology and molecular biology
  • Good language skills


Please include

  1. Curriculum vitae
  2. Diplomas (Master and PhD degree or equivalent)
  3. Research plan – description of current and future research plans
  4. Complete publication list
  5. Separate reprints of 3 particularly relevant papers

The deadline for applications is 11 June 2023, 23:59 GMT +2.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee.

You can read about the recruitment process at .

Interviews with selected candidates are expected to be held in late June/early July.

For specific information about the position, please contact the Prof. Mathias Middelboe.

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.


Application deadline: 11-06-2023
Employment start: 01-09-2023
Working hours: Full time
Department/Location: Department of Biology

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