Doctoral position (m/f/d) Institute of Experimental Medicine

Doctoral position in “Modeling Metabolic Microbiome-Host Interactions in Hydra” (f/m/d)
Research Group Medical Systems Biology, Institute of Experimental Medicine

Microbiome research has experienced vast advances in the last two decades with the advent of culture-free techniques to study the composition and function of bacterial communities. This has elucidated the importance of host-associated microbial communities for health and adaptation to changing environments. In the Research Group Medical Systems Biology at the Institute of Experimental Medicine, we use systems biological approaches incorporating a large variety of molecular data sets to better understand microbiome-host interactions and how these interactions can be therapeutically targeted. In this project, we want to understand the role of metabolic interactions on microbial community dynamics in a host-associated context. We will use the freshwater polyp Hydra as a model system to study how nutrient changes in the water column impacts the microbial community dynamics living on Hydra, and how well these changes are predicted by metabolic interactions between the community members.


Start in our Team
Join our team and support us as soon as possible, limited for 3 years.


We offer:

  • The salary will be based of the German E13 TV-L (65%) scale if terms and conditions under collective bargaining law are fulfilled
  • Part-time employment, currently 25 hours/ week
  • We offer remote and hybrid working schemes
  • Kiel University and the UKSH offer an excellent research environment on the shores of the Baltic Sea
  • You can find more exciting benefits here: Benefits ( (Information in German)


Your role:

  • As part of our highly interdisciplinary research group, you will be responsible for the integrative analysis of large-scale experimental data sets (microbiome amplicon sequencing, transcriptomics, metabolomics, genomics) in the context of microbiome-host interactions
  • Reconstruct metabolic models for the Hydra-associated bacteria from metagenomic and amplicon sequencing data using an in-house developed pipeline
  • You will use these models to simulate metabolic interactions between different members of the bacterial community in Hydra and you will validate these experiments in lab rotations with our research partners
  • Develop a new metabolic model for the host and will use metabolic modeling and experimental validation to investigate the role of the host on the metabolic factors determining community assembly


Your profile:

  • You are a highly motivated PhD candidate with the willingness to learn new and challenging methods and concepts as well as excellent (English) communication skills
  • You solve problems and have a can-do mindset
  • During your studies, you gained first experiences in bioinformatics or systems biology (omics analysis, metabolic modeling) and possess excellent programming skills (preferentially R and Python) preferably in a Linux environment
  • Further, you have experience in microbiological work and are interested in basic research with a unique model system.
  • A good command of basic statistical methods is expected, and having familiarity with machine learning/AI or a willingness to acquire these skills is regarded as advantageous
  • Knowledge of working on a central computing cluster, writing computational pipelines for analysis of large datasets, and organizing omics data and their analyses are merit.

The UKSH has set the goal to reach professional equality between all genders.


We look forward to receiving your application by October 1st, quoting the tender number 22406.


Additional Information:
For more details on the position, please get in touch with Dr. Jan Taubenheim, Institute of Experimental Medicine, Kiel University / University Hospital Schleswig-Holstein, via phone at +49-431 5000-30345 or via email at More information about the research group and the UKSH is available at and


Campus Kiel

Veröffentlicht am:  22.09.2023

Kiel, Schleswig-Holstein, DE, 24105


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Das Universitätsklinikum Schleswig-Holstein (UKSH) verbindet internationale Spitzenforschung mit interdisziplinärer Krankenversorgung. Wir sind einziger Maximalversorger und größter Arbeitgeber des Landes. Unsere mehr als 16.000 Mitarbeitenden stellen eine höchst individuelle Versorgung sicher - unverzichtbar für die Menschen in Schleswig-Holstein.

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Campus Kiel

Veröffentlicht am:  22.09.2023

Kiel, Schleswig-Holstein, DE, 24105

Ausschreibungsnummer:  22406

Haben Sie Fragen?

Ihr Kontakt zu uns:  Jan Taubenheim # 0431 - 500 30345
Recruiter:  Jessica Puton # 0431 - 500 11191 # https://rmkcdn.

Benefits am UKSH

Stellensegment: Bioengineering, Biology, Microbiology, Science, Part Time, Research