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 most if not all 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 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 stable 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 or species, 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 with other environmental bacteria, recreating the original environmental conditions, incubating the samples in a mini-bioreactor before attempting other growing conditions and testing a variety of conditions and growing media of natural 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 (1) define or develop the most appropriate growing medium that will both increase productivity of a compound and suit its downstream extraction protocole, and (2) determine the growing conditions that will lead to optimum compound production at a laboratory scale. In practice, a number of growing conditions are tested in parallel in 1-2-liter tanks that can be operated in either batch, fed-batch or continuous modes. The tanks are equipped with probes that measure temperature, pO2, pH, redox potential and glucose in real time, and analyse the exhaust gas by mass spectrometry to continuously monitor every fermentation run, standardize the production process and ultimately control the behaviour of each microbial factory.    

Bioprocess scale up

Scaling up the production of a compound can lead to a decrease in performance. Using 20-liter tanks, the fermentation engineering unit works towards standardizing the fermentation conditions to ensure a linear relationship between the culture volume and the amount of compound produced, and therefore an easy transfer of the process from a laboratory to an industrial scale (> 1m3). This work is documented in a process report to support transfer to industrial production.

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.