Automated cultivation and characterization platform

• Subject Area: Microbiology, Virology and Immunology
• Term: Funded in 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 558401136

Microbes include the key climate modulators, the best biotechnologists, the best ecosystem conservators and the best pharmacists known to mankind. Microbes for instance clean our waste(water), remediate (heavy) metal pollution and produce most clinically relevant antibiotics. These microbial capabilities will make the transition towards a knowledge-based bioeconomy possible. Collective research efforts only managed to cultivate less than 1% of microbial species that exist on Earth. To use the enormous power of microbes to solve mankind’s current problems, we need to get more of them in hand so we can work with them. The current proposal describes a platform that makes cultivation of new microbes possible at an unprecedented scale, by automating cultivation. To achieve this, we will use our decade-long experience in refining cultivation techniques at the manual scale elucidating >150 novel bacteria, as we now have all knowledge to propel microbial cultivation into the era of automatized, high-throughput biology. The tailor-made automated cultivation & characterization platform takes (pre-enriched) environmental samples, distributes them over 384-well plates with specialized growth media, incubates the plates at the right conditions and automatically monitors growth to decide which wells show signs of harbouring a growing culture (of novel origin), to then supply these with additional nutrients. Once cultivation has yielded axenic cultures of novel bacteria, these will be deposited in multiple microbial culture collections, to make these valuable bioresources accessible to researchers and companies in Germany and around the world. The platform then starts a second phase, in which optimal growth conditions are determined, to ensure that the novel species can immediately be implemented into research towards applications, for instance in bioremediation, the discovery of novel antibiotics or restoring health of forests. The platform requested here will further strengthen the already strong infrastructure in Jena in the field of Microbiology, as a key part of the FSU’s Life profile area. Microbiology research takes a central role in two Jena-led DFG-funded CRCs (ChemBioSys and AquaDiva) and is the central theme of the DFG-funded Cluster of Excellence ‘Balance of the Microverse’. By delivering characterized novel microbial strains the platform provides a very important basic step in supplying research initiatives in Jena, as well as research groups and companies beyond, with these important untapped bioresources to strengthen our knowledge and find applications in the bioeconomy.

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: Automatisierte mikrobielle Kultivierung- und Charakterisierung Plattform
• Instrumentation Group: 3520 Bakterien-Zuchtgeräte, Fermenter
• Applicant Institution: Friedrich-Schiller-Universität Jena
• Leader: Professor Dr. Christian Jogler