PhD position in Metabolic microbiome modelling Research Group Medical Systems Biology, Institute of Experimental Medicine

The University Medical Center Schleswig-Holstein is one of the largest university hospitals in Europe with more than 80 clinics and institutes. It offers outstanding medical treatment and excellence in research and education with more than 17,000 employees. We provide top research at the interface of medicine, science and technology and maintain research co-operations with universities all over the world.

The research group Medical Systems Biology at the Institute of Experimental Medicine uses systems biological approaches incorporating a large variety of molecular data sets to gain a deeper understanding of the role of the microbiome in host health and disease and how it can be used as a therapeutic target to treat human diseases. In this context, one key methodology that we are using is constraint-based metabolic modelling approaches.

Start in our team:
We are looking for professional and competent support to start as soon as possible, limited to three years with the possibility of further extension.

Your role:

• In this interdisciplinary project, you will integrate large-scale microbiome, transcriptomic, metabolomic and genomic data to explore metabolic interactions in gut bacterial communities
• Your main goal will be to reveal the "dark matter” of unknown cross-feeding interactions in the minimal model microbiome SIHUMIx and to understand how these connections influence which species thrive
• Using experimental data from our partner lab (Martin von Bergen, UFZ Leipzig), you will build a computational model of SIHUMIx to predict new interactions and how the community reacts to disturbances—predictions that will later be tested in bioreactor experiments
• This work will give us a much clearer picture of how gut bacteria support one another and how these networks can reorganize under changing conditions
• This project is set within the wider scope of the DFG-funded priority research area "Illuminating Gene Functions in the Human Gut Microbiome” that combines microbiome researchers across Germany

Your profile:

• We are looking for a highly motivated PhD student (m/f/d) with a background in bioinformatics, systems biology, molecular biology or a related field
• You should have strong programming skills (preferably in R and Python) and familiarity with Linux
• Experience in constraint-based metabolic modeling, next-generation sequencing data analysis (RNA-Seq, scRNA-Seq, metagenomics) and statistics is essential
• Given the international nature of our research group, excellent communication competence in English is required

We offer:

• The salary will be based on the German E13 TV-L scale (75%), if terms and conditions under collective bargaining law are fulfilled
• Part-time employment, currently 28,75 hours/week
• A family-friendly working environment with a commitment to improving the work-life balance
• You will have access to a variety of programs supporting PhD students at Kiel University that also include diverse soft-skill courses

The UKSH has been certified as a family-friendly institution and is committed to further improving the compatibility of work and family life. We support the employment of disabled persons. Persons with disabilities will, with appropriate qualifications and aptitudes, be employed preferentially. The UKSH has set the goal to reach professional equality between men and women. The University aims to increase the number of women among the faculty staff and therefore explicitly encourages the application of female scientists.

Additional information:

Please submit your application until 7th January 2026 , indicating the reference number 27635 , via our online portal:

Apply now!
https://jobs.uksh.de/job/Kiel-PhD-position-%28mfd%29-in-%E2%80%9EMetabolic-microbiome-modelling-Schl-24105/1273528701/