High-Throughput Genetic Analysis of Single Cells Using Microfluidically Generated Hydrogels

Abstract

Typical metagenomic datasets characterize populations as a whole by sequencing all the DNA fragments present in a sample, and are therefore unable to identify different genes as having originated from the same cell or distinct cells. We address this problem by microfluidically encapsulating single cells in hydrogels, amplifying the genomic DNA inside water-in-oil emulsion droplets, sorting out those cells carrying a gene of interest, and sequencing the gene at the single-cell level. Our method is broadly applicable to standard DNA amplification techniques, including polymerase chain reaction (PCR) and multiple displacement amplification (MDA). Since our method does not require cell culture, it is particularly useful for studying unculturable bacteria populations such as those found in the human gut and environmental water sources, and could be extended to determine which species or strains carry a rare metabolic gene.