Microbial robustness 101: tools and applications

Conference poster, 2022

Striving for a fossil-free society, bio-production is gaining increasing interest over time. Bioproduction applies microorganisms (bacteria, yeast, fungi) to produce valuable chemicals from different raw materials (plant biomass, waste materials, etc.) and offers sustainable use of side-streams and/or waste streams. Bioproduction suffers from challenges such as poor microbial performance and reproducibility. One key feature in this field is microbial robustness, i.e., the stability of a phenotype (cellular function) when a system is challenged by different perturbations. Microbial robustness, due to its abstract nature, has been poorly studied also due to the lack of tools available. Moreover, being able to include robustness evaluation in the early stages of bioprocess and strain design would facilitate their scaling up from the laboratory- to the industrial scales.

Here two tools to explore microbial robustness with some applications and case studies in Saccharomyces cerevisiae are presented. First, a way to quantify the robustness of cellular functions was developed. The robustness coefficient proposed allows comparison between strains and cellular functions in a given perturbation space. This method, based on the Fano factor, is dimensionless, free from arbitrary control conditions and frequency-independent. Second, fluorescent biosensors sensing the intracellular environment were developed into a versatile and easy-to-use toolbox. Such toolbox was used in population studies to identify different physiological responses in different strains exposed to industrially-relevant media and conditions. In the future, it will be implemented in single-cell analysis in microfluidic devices and for studying the formation of subpopulations in large-scale fermentations.

All together, these tools will give the possibility to identify robustness traits and mechanisms, allowing for physiological insights that are a foundation for improving industrial strains and process designs.