Droplet microfluidic PicoSorter for high throughput and active selection of cellulolytic microorganisms

Classical enrichment methods for microorganisms rely on growth in selective media, but such practices are relatively expensive, low-throughput, and may result in a biased representation of taxa. Alternatively, microorganisms can be cultivated in thousands of picoliter droplets of equal volume, with the most efficient strains selected through quantitative assays at unprecedented ultrahigh throughput. Here, we present a novel high-throughput microfluidic technology for the characterization of cellulolytic microbial communities at the single-cell level. Individual microbial cells are encapsulated in picoliter droplets for clonal cultivation, after which a colorimetric assay using Congo red is applied to identify positive droplets containing cellulose-degrading strains. These positive droplets are then actively sorted at high throughput using absorbance-activated droplet sorting. The critical component of the enrichment assay we propose is the PicoSorter module, which expands the range of available droplet-based enrichment methods. The platform introduces a new design that enables buffer picoinjection required for the assay, followed by droplet sorting on a millisecond timescale.