PhD position (m/f/d) in „Metabolic microbiome modelling"

Research Group Medical Systems Biology, Institute of Experimental Medicine

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 as well as 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 are constraint-based metabolic modelling approaches.

Start in our Team

We are looking for professional and competent support to start as soon as possible, limited for 3 years with the possibility of a further extension.

What 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 work-life balance
• You will have access to a variety of programs supporting PhD students at Kiel University also including diverse soft-skill courses
• You can find more attractive UKSH benefits here: Benefits (uksh.de)

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 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 skills in English are required

We are looking forward to your application. Please submit your application until January 7th, 2026 indicating the reference number 27635.

Additional Information:

For more details on the position, please contact Prof. Dr. Christoph Kaleta, Institute of Experimental Medicine, Kiel University / University Hospital Schleswig-Holstein, via phone at +49-431 500-30340 or via email c.kaleta@iem.uni-kiel.de. More information about the research group and the UKSH is available at https://www.iem.uni-kiel.de/msb and www.uksh.de/karriere.