PhD fellowship in Nutrition and Gut Microbiome Research

Department of Nutrition, Exercise and Sports invites applicants for a PhD fellowship in Nutrition and Gut Microbiome Research. The PhD position is part of the project GutEnergy – Human gut microbiome-dependent energy extraction, which is supported by the Novo Nordisk Foundation.

Start date is expected to be 15 October 2024 or as soon as possible thereafter.

The project
The project builds on our previous work suggesting that differences in gut microbiome community structures may affect energy extraction (Boekhorst et al. 2022; Microbiome Background video here:

The GutEnergy project will investigate whether differences in gut microbiome community structures affect excretion of dietary calories in faeces by conducting a human dietary intervention study and combining traditional faecal measurements, bomb calorimetry, and state-of-the-art omics technologies (i.e. microbiome and metabolomics).

In your role as PhD student, you will be in charge of writing the study protocol for approval to the Ethical Committee. Following approval, you will be responsible with the recruitment of study participants and for conducting  the controlled dietary intervention study, which includes examination visits and handling of biological samples. Furthermore, you will conduct liquid chromatography mass spectrometry-based metabolomics, bomb calorimetry, and microbiome analyses on collected biological samples. Finally, you will integrate microbiome, metabolomics, and faecal energy data, and write scientific publications.

The position involves collaborative work with Prof. Michiel Kleerebezem and his team at Wageningen University & Research, The Netherlands.

Who are we looking for?
We are looking for motivated candidates within the fields of Human Nutrition, Bioinformatics, Biology, Biochemistry, Biotechnology, Analytical Chemistry or similar field who has a keen interest in nutrition, microbial ecology, microbiome and metabolomics.

Our group and research - what do we offer?
You will be part of the Nutrition, Microbiome and Metabolomics Group headed by Associate Professor Henrik Munch Roager at Department of Nutrition, Exercise and Sports, Faculty of Science at University of Copenhagen. We offer a dynamic, sociable, collaborative, and international environment with exciting scientific challenges and opportunities to develop your scientific career. The core of our research is to perform high quality human dietary interventions and cohort studies with a strong emphasis on measuring diet-microbiome interactions through metabolomics.

The research group is also affiliated to the Copenhagen Gut Microbiome Hub, which brings together the region’s leading scientists, researchers and industry professionals dedicated to leverage the gut microbiome to improve health.

The University is situated in Copenhagen, which is consistently rated among the world's top 10 most livable and sustainable cities. Life for families is made easier via a publicly supported daycare and healthcare system, dual-career opportunities, maternity/parental leave, and six weeks of annual vacation. International candidates may find useful information on living and working in Denmark. Useful information is also available at the university’s International Staff Mobility (ISM) office, which offers a variety of services to international researchers coming to and working at the University of Copenhagen.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Principal supervisor is Associate Professor Henrik Munch Roager (, Department of Nutrition Exercise and Sports, University of Copenhagen.

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. MSc degree in Human Nutrition, Bioinformatics, Biology, Biochemistry, Biotechnology or similar field. 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 program

  • 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 (3-6 months) at Wageningen University & Research, The Netherlands
  • 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:

  • A MSc degree in Human Nutrition, Bioinformatics, Biology, Biochemistry, Biotechnology or related fields with excellent results. Applicants expecting to obtain the MSc degree in the near future are also encouraged to apply.
  • The candidate will be self-motivated with the ability to work independently as well as competent to collaborate as part of an interdisciplinary team.
  • A creative and curious mindset and a strong drive
  • Excellent communication skills in both spoken and written English.
  • Excellent communication skills in Danish (or related Nordic language) is an advantage

Prior experience and hands-on in any of the following areas is an advantage:

  • Hands-on experience with human intervention/cohort studies
  • Liquid chromatography mass spectrometry
  • Omics data analysis, statistics and R programming

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 available)
  5. Reference letters (if available)

Application deadline:
The deadline for applications is 4 August 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. 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 during the period 19th-23th of August, 2024.

For specific information about the PhD fellowship, please contact the principal supervisor Associate Professor Henrik Munch Roager (

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. 


Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.


Henrik Munch Roager


Ansøgningsfrist: 04-08-2024
Ansættelsesdato: 15-10-2024
Arbejdstid: Fuldtid
Afdeling/Sted: Department of Nutrition, Exercise and Sports
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