Advanced Microbial Cultivation and Microbiome Metabolomics

This research area aims to advance microbiome-based drug discovery by developing scalable cultivation and biofermentation strategies to study microbes associated with fungal pathogens. It integrates high-throughput approaches with analyses of metabolic interactions and environmental influences to uncover how microbiome dynamics shape antimicrobial activity and resistance.

The Bio Pilot Plant (BT)  develops and provides innovative bioprocess strategies for access and biotechnological usage of natural products. Besides this, we are experts in online monitoring of cultivations to gain deep insights into microbial growth processes and interactions, including co-cultures. The BioPilotPlant is currently coordinating the Priority Programme "eBiotech" funded by the Deutsche Forschungsgemeinschaft and the consortium "SynThera" funded by the Carl Zeiss Foundation, and is an active participant in Priority Programme "InterZell", the Leibniz Center for Photonics in Infection Research LPI, the German Center for Infection Research DZIF, the EU-funded project "UpCycle", and the Cluster of Excellence "Balance of the Microverse".

A key research interest of BT revolves around small, diffusible redox-active natural products and their potential biotechnological usage. Redox-active natural products play a key role in energy metabolism, and if they can cross the cellular membrane, they can be employed to link cellular metabolism to the abiotic surroundings of bioprocess technology, e.g., in bioelectrochemical systems. We therefore work at the interface of bioprocess technology, microbial physiology, molecular engineering, and electrochemistry to identify, study, and utilize redox-active natural products for innovative bioprocess development. Fungi are well known for producing such metabolites, but they have hardly been explored for biotechnological use.

We are seeking an excellent and enthusiastic postdoctoral researcher with a strong interest in natural product microbiology for biotechnological innovations. The specific focus of the project should align with the objectives of the aforementioned consortia.

Your profile:

• PhD degree in Microbiology, Chemical Biology, Biotechnology, Biochemistry, or a related discipline
• Knowledge and experience in the investigation of microbial physiology or redox biochemistry
• Knowledge or strong interest in bioprocess technology

The Department Deep Microbiome Metabolomics (DMM) investigates gut microbial metabolism and its interactions with medications, nutrition, and human physiology. We study these processes across different levels of biological organization, from complex microbial communities to individual strains and down to the genes involved. To mechanistically dissect microbiome functions, DMM applies state-of-the-art approaches including high-throughput phenotypic screening, metabolomics, and advanced in vitro host models. The DMM aims to develop a fundamental understanding of how perturbations shape the structure and functions of the gut microbiome, and to advance functional microbiome research and translational medicine.

A key interest of DMM is to uncover how microbial interactions translate into measurable metabolic outputs that impact host physiology. While bacterial contributions to gut metabolism have been widely studied, the fungal component (the mycobiome) and its interplay with bacteria remain comparatively understudied, despite growing evidence that cross-kingdom interactions can shape colonization, community stability, metabolic pathways, and host responses. We therefore seek an excellent and highly motivated post-doc candidate to mechanistically investigate bacterial–fungal interactions in a host-specific context using advanced metabolomics technologies, including spatial metabolomics. The project will integrate controlled microbial community models (including defined bacterial–fungal co-cultures) with host-relevant systems and cutting-edge mass spectrometry-based readouts to identify interaction-driven metabolites, map their spatial distribution, and link these signatures to microbial functions and host outcomes.

Your profile:

• PhD degree in Microbiology, Systems Biology, Bioinformatics, Analytical Chemistry, Biochemistry, Chemical Biology, or a related discipline
• Experience with (or enthusiasm to learn) metabolomics workflows and mass spectrometry-based data analysis; experience in spatial metabolomics is a plus
• Hands-on experience in microbial cultivation (anaerobes and/or fungi), co-culture experiments, or gnotobiotic/host-associated models is advantageous