PhD Student (m/f/d) in microbiome and multi-omics analyses (IKMB)

Within the EU-funded research consortia PerPrev and 3TR, a PhD student position is available at the Systems Immunology Lab of the Institute of Clinical Molecular Biology (IKMB), which is part of the University Hospital Schleswig-Holstein (UKSH) and Christian-Albrechts-Universität zu Kiel (CAU).

The successful candidate will work on projects focusing on the role of the gut microbiome in inflammatory bowel disease (IBD) and the integration of multi-omics datasets to uncover mechanisms underlying disease progression and therapy response. The main aim is to understand how microbial communities and their functional potential shape immune regulation and impact therapeutic outcomes.

Start in our team

We are looking for professional and competent support to start as soon as possible, limited for 3 years.

What we offer:

• The salary will be based on the German E13 TV-L scale, if terms and conditions under collective bargaining law are fulfilled
• Part-time employment currently 25 hours/week
• The opportunity to pursue a PhD in a highly interdisciplinary and international environment
• Access to unique, large-scale clinical and multi-omics datasets from IBD cohorts within PerPrev and 3TR.
• Training opportunities in advanced bioinformatics, systems immunology, and microbiome research.

Your role:

• Analysis of large-scale microbiome datasets (16S rRNA sequencing, metagenomics, MAG reconstruction)
• Integration of multi-omics datasets (metagenomics, metatranscriptomics, metabolomics, host transcriptomics)
• Developing computational strategies to link microbial and host features to therapeutic response in IBD patients
• Close collaboration within international research consortia and with clinical partners

Your profile:

• A completed academic degree (Master or equivalent) in engineering, mathematics, bioinformatics, computational biology, systems biology, biostatistics, or related areas
• Solid experience in bioinformatics and data analysis of different omics layers. Specific knowledge on microbiome analysis, including MAG reconstruction and 16S data analysis, is a plus
• Strong programming and data analysis skills (R and/or Python required; experience with HPC environments is advantageous)
• Enthusiasm for multi-omics data integration and systems medicine approaches.
• Excellent English communication and writing skills.

Please submit your application until 11th November 2025, indicating the reference number 27491.