Agarose gel microcapsules enable easy-to-prepare, picolitre-scale single-cell genomics, yielding near-complete genome sequences

Abstract A novel type of agarose gel microcapsule (AGM), consisting of an alginate picolitre sol core and an agarose gel shell, was developed to obtain high-quality single-cell amplified genomic DNA of bacteria. The AGM is easy to prepare in a stable emulsion with oil of water-equivalent density which prevents AGM aggregation, with only standard laboratory equipment. Single cells from a pure culture of Escherichia coli , a mock community comprising 15 strains of human gut bacteria, and a termite gut bacterial community were encapsulated within AGMs, and their genomic DNAs were obtained with massively parallel amplifications in a tube. The genome sequencing did not need second-round amplification, and showed an average genome completeness that was much higher than that obtained by the conventional amplification method in microlitre scale, regardless of the genomic guanine-cytosine contents. Our novel method using AGMs allows many researchers to perform single-cell genomics easily and effectively, and can enhance the genome analysis of yet-uncultured microorganisms.