Fermentation engineering

Taming the Unkown, optimizing yields

Discovery and production of an active compound requires a great work of optimization to define the most appropriate growing conditions for often previously uncultivated microbial species. Upstream in the discovery process, before bioactivity screening and compound identification, the fermentation engineering hub needs to determine the optimal and sometimes original conditions that will sustain growth of a large amount of the bacterial species present in an environmental sample. Once a compound with a given activity has been identified, the team needs to search for the fermentation conditions that will minimize or take advantage of the microbial stress and activate the right metabolic pathways involved in the biosynthesis of the compound. This process is important to identify the critical parameters that influence product yield and quality, a pre-requisite to guarantee repeatable and robust compound production at an industrial scale.

Core activities

Advanced bacterial cultivation

Highly diverse and previously uncultured bacterial strains sampled in the environment need to be isolated before performing biological activity screens. The fermentation engineering hub works in collaboration with the biodiversity farming unit to understand the unique behavior of each strain, and find the conditions necessary to grow them in a laboratory setting. This is achieved using a panel of growing techniques on solid and liquid media: performing cocultures, recreating the original environmental conditions, and testing a variety of conditions and growing media of complex or synthetic origin.

Bioprocess optimization

Each bacterial strain needs to be challenged in a unique way to enhance the production of an endogenous metabolite or to induce the biosynthesis of a new compound. To optimize production performances, the fermentation engineering hub proceeds stepwise to define or develop the most appropriate growing medium that will (1) lead to optimal  compound production at a laboratory scale, and (2) suit its downstream extraction protocol. In practice, different growing conditions  are tested in parallel in  2-liter tanks that can be operated in either batch, fed-batch or continuous modes. The tanks are equipped with one-line probes that measure temperature, pO2, pH, redox potential, and analyze the exhaust gas by mass spectrometry to continuously monitor every fermentation run, standardize the production process and ultimately control the behavior of each microbial factory.    

Bioprocess scale up

Scaling up the production of a compound can lead to a modification  in strain performances. Using 20-liter tanks, the fermentation engineering unit works towards standardizing the fermentation conditions to optimize strain productivity and improve compound production titer, yield and quality. The ultimate goal is to allow for easy transfer of the process from a laboratory to an industrial scale (> 1m3). The optimization process is documented in a process report and the transfer is accompanied by Deinove’s fermentation unit members to ensure it runs smoothly. 

Support activities

In collaboration with the synthetic biology hub, early-step optimization of compound production by iterative rounds of genetic and fermentation engineering.  


Kent, J. A. (2003). Industrial Fermentation: Principles, Processes, and Products. In Riegel’s Handbook of Industrial Chemistry (pp. 963–1045). Springer US.

Schmidt, F. R. (2005). Optimization and scale up of industrial fermentation processes. Applied Microbiology and Biotechnology, 68(4), 425–435.

Fedorenko, V. (2015). Antibacterial Discovery and Development: From Gene to Product and Back. BioMed Research International. 1–16.