The Friedrich Schiller University Jena is a dynamic and innovation-driven university centrally located in Germany. With a broad range of disciplines, it shapes the future through excellent research and teaching. Its scientific excellence is reflected in the profile areas Light - Life - Liberty, which provide pioneering insights and sustainable solutions for the society of tomorrow. Through close collaborations with leading research institutions, innovative companies, and renowned cultural organizations, it advances interdisciplinary developments. With around 17,000 students and approximately 10,000 employees, it defines Jena as a vibrant, internationally connected city of science and innovation.

The Microbiome Dynamics Group at the Institute of Microbiology seeks to fill the position of a

PhD Position in Microbiome Systems Biology



commencing on 1st of March, 2026.
We offer a part-time position (65%, 26 hours per week), limited to 4 years.

The research group Microbiome Dynamics (MBD) is seeking an excellent and enthusiastic Ph.D. student for high-risk-high reward research in the fields of metagenomics and big data integration. MBD is an active participant in several national and international collaborative efforts to the interplay between the host, symbiotic communities, and pathogenic species. Together with renowned scientists and supported by an excellent infrastructure you will have the opportunity to make an important contribution toward a healthier society. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility. The Ph.D. project is framed on the new collaborative research project “SynThera” (http://www.synthera.eu/), and the specific objective is to integrate shotgun metagenomics data with genome-scale metabolic modeling, using machine learning methods for proposing novel strategies to increase colonization potential of engineered probiotics strains in the human gut.

You will also:

Contribute to several national and international research projects focused on the role of the microbiome in globally significant diseases
Contribute to sharing your knowledge through publications, conference presentations, and outreach activities
Work towards the completion of a PhD based in the project’s research area

A strong interest in conducting collaborative research on the topic outlined above is paramount
Candidates are expected to be interested in working at the boundaries of several research domains
Master's degree in Computational Biology, Bioinformatics, Systems Biology, Bioengineering, Chemical Engineering, or a related discipline
Knowledge and experience in the analysis of metagenomics and/or biological high-throughput data
Knowledge of statistical methods in the context of biological systems
Experience with programming (Python, Perl, C++, R)
Well-developed collaborative skills


Are you hesitating because you don't meet one or some of our requirements? Please do not hesitate to apply and give us a chance to get to know you.
The successful candidate will be hosted in the research group Microbiome Dynamics of Prof. Dr. Gianni Panagiotou (https://www.leibniz-hki.de/en/microbiome-dynamics.html) in an international, dynamic team, and an “open-door” atmosphere with access to state-of-the-art computational resources.

MBD is currently coordinating the EU-funded consortium MiCCrobioTAckle (https://miccrobiotackle.eu/), the BMBF-funded consortium PerMICCion (www.permiccion.de), and is an active participant in the EU-funded consortia FOODGUARD and NUTRIMMUNE, the Cluster of Excellence \"Balance of the Microverse\" (www.microverse-cluster.de), and the CRC/Transregio 124 \"Pathogenic fungi and their human host: Networks of interaction\" (www.funginet.de) funded by the DFG and the consortium SynThera funded by the Carl Zeiss Foundation.
We offer an international and multi-disciplinary environment with strong expertise in the proposed re...