Encapsulating Yeast in Agarose Microparticles for High Throughput Microcolony Analysis

Yeasts and fungi are powerful hosts to produce numerous value-added chemicals. Metabolic engineering efforts in yeasts can be coupled with high-throughput analysis platform to effectively analyze and select desired phenotypes. However, choices of analyzing yeast cells using high-throughput are still limited. Traditional plate based colony screening can be non-quantitative and time-consuming while FACS based single cell screening can be associated with high false positive rate. To provide an alternative method for high-throughput analysis in yeasts, we performed experiments in a droplet microfluidic platform. We encapsulated single yeast cells into pico to nano-liter sized agarose droplets and allowed them to culture and to form isolated microcolonies in agarose microparticles. These microparticles can then be analyzed by high-throughput analysis platform such as flow cytometry and next generation sequencing. This workflow enables a quantitative and high-throughput analysis of yeast colonies.