The Department of Food Science, Section of Microbiology, Gut Health, and Fermentation invites applicants for a PhD fellowship in Gut ecology and Phage Encapsulation with the aim of exploring innovative approaches to gut microbiome modulation using bacteriophage-based therapies and to develop novel drug delivery strategies for bacteriophages.

The PhD position is part of a Sapere Aude research project funded by the Independent Research Fund Denmark: ‘ PhageX : Next-generation bacteriophage therapy for treating gut-related diseases’ ()

Start date is (expected to be) 1st of August 2024 or as soon as possible thereafter.

The project

During the last decade it has become evident that a range of complex diseases are associated with gut microbiome (GM) imbalances, amongst other metabolic syndrome, colon cancer, autism spectrum disorders, and inflammatory bowel disease (IBD). This makes the GM an attractive therapeutic target for faecal microbiota transplantation (FMT), but widespread use of FMT is unlikely due to inconsistent treatment outcomes and the risk of infection by bacteria and human viruses that are transferred along with the donor material. Recent studies point at the bacterial viruses (bacteriophages, in short phages) as the driving element for successful FMT. The PhageX project is based on the bold hypothesis that phage transplantation not only can have same effect as FMT, but it can also be transformed into a reproducible production of safe phage therapeutics that warrant low risk of infection of pathogenic bacteria and human viruses from the donor material. Both in vitro simulations of gut conditions and animal models will be applied to evaluate the methodologies. Although IBD will be used as a proof-of-concept case, PhageX will open a myriad of possibilities to cure various GM-related diseases with minimal risk for the patient and thereby replacing FMT with a next-generation phage-mediated therapy.

The project is built on an exciting collaboration between Tallinn Technical University, Estonia, Amsterdam UMC, The Netherlands, and Section of Experimental Animal Models at the University of Copenhagen.

Specific tasks for the PhD position in Gut ecology and Phage Encapsulation

Develop a method for gentle encapsulation of bacteriophages
Chemostat fermentations of intestinal content
Working with in vitro intestinal models
Creating a protocol for improved matchmaking between donor bacteriophages and recipient gut microbiome
In vivo animal studies and collection of samples. It is noted that the assistance from experienced personnel will be provided as required until ABD license in laboratory animals science have been obtained
Gut microbiome analysis
Initiating your engineering creativity

Who are we looking for?

We are looking for candidates within a relevant field, such as biotechnology, pharmaceutical, and food science.

Our group and research- and what do we offer?

The selected PhD fellow will be part of the Section of Microbiology, Gut Health, and Fermentation. We are located in Frederiksberg, Copenhagen.

The section currently has ~50 members and offers an open, supportive environment for everyone to thrive. There will be a strong focus on work-life-balance. Currently there are ~18 PhD students in the section representing many different nationalities, which provide a friendly and useful network for the PhD students. At both department and university level there are also yearly social and career relevant events targeting PhD students. You will also be part of our exciting social events in the section. As a member of the group, you will participate in our biweekly section meetings, where you will have the opportunity to present your work in a safe environment and engage in scientific discussions relevant to our field.

In the section we work on a range of topics that range from gut health, food fermentation and starter culture functionality, food preservation and spoilage including biocontrol, microbial food safety and hygiene, gut microflora and probiotics in humans and animals, and microbiological quality assurance. The department hosts comprehensive infrastructure, well-equipped facilities, and extensive experience in phage biology, colloid research for food properties, and microbiome investigation over decades. While expertise in anaerobic culturing for microbiome studies have been developed the last decade, utilizing e.g. anaerobic chambers and Hungate systems. Additionally, the department is equipped with an in-house in vitro colon model, the CoMinigut, that are used for assessing dietary influences on gut microbiota and metabolite production. The presence of four sets of 2L Sartorius Biostat A bioreactors underline the ability to carry out controlled fermentation experiments. Moreover, our state-of-the-art gut virome pipelines, encompassing sample preparation and analysis, include a robust third-generation sequencing setup, built on Oxford Nanopore technology. Collaboration extends beyond Food Science, with several clinical partners specializing in gastrointestinal diseases as well as experts in animal models, that offers all required facilities. The synergy of these collaborations enriches our research endeavours.

Principal supervisor:

Associated Professor Jens Risbo, Department of Food Science, University of Copenhagen. E-mail:

jri@food.ku.dk , Direct Phone: +4535333224.

The PhD programme 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.

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. food science, microbiology, pharmaceutical science, and biotechnology. 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.

General 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 stays at other research institutions, which for this position will be in both Estonia (3 months) and The Netherlands (3 months)
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 a candidate with several (not all) of the following qualifications:

An MSc degree in areas relevant to the PhD project (e.g., food science, microbiology, pharmaceutical science, and biotechnology)
Curious mindset with strong interest in the importance of our gut microbiome in health and disease
Practical experience in in-vitro microbiology including bacteriophage assays and batch/chemostat fermentations.
Bioinformatics analysis of bacterial and viral metagenomes and experience in using R- and/or Python for data analysis.
Experience within material science and physical chemistry
Keen to work with laboratory animals (only mice)
Excellent English communication skills both written and orally
Good interpersonal skills
Strong work ethics
High ambitions
Team player

Key selection criteria:

Professional qualifications relevant for the position
Find it exciting to work in a highly multidisciplinary project
Relevant work experience
Language skills
Creative thinking
Level of enthusiasm and motivation
Ability to work independently

Application and Assessment Procedure

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

Please include :

Motivated letter of application (max. one page)
Your motivation for applying for the specific PhD project
Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
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.
Publication list (if possible)
Reference letters (if available)

Application deadline:

The deadline for applications is 31 May 2024, 23:59 GMT +2.

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 week late May or early June 2024.

Questions
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.

PhD fellowship in Microbiology and Phage Delivery Engineering