Quantifying the effects of cell death and agar density on yeast colony biofilms using an extensional-flow mathematical model

We use a combination of experiments, mathematical modelling, and parameter estimation to better understand how agar density affects colony biofilm growth of the yeast species Saccharomyces cerevisiae . We obtained 15 total experimental replicates on rectangular plates filled with 0.6%, 0.8%, 1.2%, and 2.0% agar. In the experiments, we measured the horizontal expansion over time, the number of living cells, and the colony-biofilm aspect ratio. These measurements quantify the colony-biofilm size, composition, and shape, respectively. We modelled colony-biofilm expansion using a thin-film extensional-flow mathematical model. By fitting five unknown model parameters to mean experimental data, we show that nutrient uptake decreases and biofilm–substratum adhesion strength increases with an increase in agar density. Sensitivity analysis, fitting to individual replicates, and synthetic-data analysis confirmed that increased biofilm–substratum adhesion is the most consistent effect of increased agar density. This finding aligns with similar results reported for bacteria, and suggests that substratum mechanics are important for yeast-colony-biofilm growth.