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 DNA samples were prepared 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 using a conventional amplification method on the microlitre scale, regardless of the genomic guanine–cytosine content. Our novel method using AGM will allow many researchers to perform single-cell genomics easily and effectively, and can accelerate genomic analysis of yet-uncultured microorganisms.

开发了一种新型琼脂糖凝胶微胶囊 (AGM)，由藻酸盐皮升溶胶核和琼脂糖凝胶壳组成，以获得高质量、单细胞、扩增的细菌基因组 DNA。AGM 很容易在稳定的乳液中与水等效密度的油一起制备，从而防止 AGM 聚集，仅需标准实验室设备。来自大肠杆菌纯培养物的单细胞，一个包含 15 株人类肠道细菌的模拟群落和一个白蚁肠道细菌群落被封装在 AGM 中，并且它们的基因组 DNA 样本是通过在试管中进行大规模平行扩增制备的。基因组测序不需要第二轮扩增，并且无论基因组鸟嘌呤 - 胞嘧啶含量如何，其平均基因组完整性均高于使用传统扩增方法获得的微升级别。我们使用 AGM 的新方法将使许多研究人员能够轻松有效地进行单细胞基因组学，并且可以加速对尚未培养的微生物的基因组分析。