Development and application of droplet microfluidics for high-throughput single-cell and single-molecule genomics

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Genome sequencing is an extremely powerful tool for understanding biology. However, a relatively large amount of DNA, usually obtained by growing a large clonal population of cells under laboratory conditions, is required for this approach to work. This is difficult, or simply impossible, for the vast majority (>99%) of microorganisms that resist cultivation attempts. The overall objective of this proposal is to develop a novel high-throughput method for rapidly identifying and sequencing individual DNA molecules or complete bacterial genomes from targeted single-cells of interest within a large population. By taking advantage of droplet-based microfluidics, in which every sub-nanoliter droplet is equivalent to a reaction tube that can be manipulated, it will be possible to dramatically improve current single-cell whole-genome amplification and metagenomics methods while offering exciting new possibilities such as ultra high-throughput labeling and retrieving of droplets based on the presence or absence of specific genetic markers.