研究人员提出了Microbe-seq，这是一种高通量方法，可以从复杂的微生物群落中产生单个微生物的基因组。他们用微流体将单个微生物封装在液滴中并释放它们的DNA，然后对其进行扩增，用液滴特异性标签标记扩增产物，并进行测序。研究人员探索人类肠道微生物组，对来自单个人类供体的20,000多个微生物单扩增基因组（SAG）进行测序，并对100种细菌的基因组进行组装，其中包括几种具有多个亚种菌株的细菌。
他们使用这些基因组来探测微生物的相互作用，重建水平基因转移（HGT）网络并观察92个物种对之间的HGT；他们还发现crAssphage和一株硫化杆菌之间存在显著的体内宿主-噬菌体关联。Microbe-seq提供高通量免培养能力，以单微生物的分辨率研究复杂微生物群落的基因组蓝图。
据介绍，用单细胞分辨率描述复杂的微生物群落一直是微生物学的一个长期目标。
附：英文原文
Title: High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Author: Wenshan Zheng, Shijie Zhao, Yehang Yin, Huidan Zhang, David M. Needham, Ethan D. Evans, Chengzhen L. Dai, Peter J. Lu, Eric J. Alm, David A. Weitz
Issue&Volume: 2022-06-03
Abstract: Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.
DOI: abm1483
Source: https://www.science.org/doi/10.1126/science.abm1483