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 November, 2025.
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.

Your responsibilities:

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

Your profile:

• 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.

We offer:

• 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 research field. Currently, the group consists of approximately 15 members at different levels of seniority.
• Comprehensive support for doctoral researchers through the Graduate Academy as well as our local and international network.
• Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) at salary scale E-13 — depending on the candidate’s personal qualifications—, including a special annual payment in accordance with the collective agreement.
• 30 days of vacation per calendar year plus two days off on December 24 and 31

This is a part-time position (65%, 26 hours per week) offered as a fixed-term position for 4 years.

Candidates with severe disabilities will be given preference in the case of equal qualifications and suitability.

Are you eager to work for us? Then apply by 31.08.2025 using our online form.