Science:微生物高通量单细胞测序,助力在菌株水平上解析肠道菌群
创作:mildbreeze 审核:mildbreeze 07月01日
  • 开发具有菌株分辨率的微生物高通量单细胞测序方法Microbe-seq,该方法结合了基于液滴的微流控技术和专有的生信分析流程,能从复杂菌群中获得单个细菌的基因组信息;
  • 用该方法分析人肠道菌群样本,得到21914个单细胞微生物基因组信息,组装出76个物种水平基因组(52个为高质量),发现10个物种含有多个菌株,并组装了菌株水平的基因组;
  • 用这些基因组分析了菌群多样性,构建了菌群的水平基因转移网络(发现HGT主要发生在同菌门的菌株之间),并探索了噬菌体与宿主菌的相关性(发现crAssphage只与一个普通拟杆菌菌株有明显关联)。
主编推荐语
mildbreeze
肠道菌群是复杂的微生物群落,典型的人肠道菌群可包含数百个微生物物种,而每个物种中又可能包含多个有功能差异的菌株。然而,在菌株水平上开展大规模的肠道菌群研究,目前在方法学上仍存在挑战。为了克服这一困难,哈佛大学David Weitz团队与麻省理工学院Eric Alm团队合作,开发了一种新的微生物高通量单细胞测序方法Microbe-seq,无需培养即可从复杂群落中获得大量的单个微生物基因组信息,解析出菌株分辨率的高质量微生物基因组,并以人肠道菌群分析为例展示了该方法在菌群研究领域中的巨大潜力。相关论文已于Science发表,郑文山博士和赵诗杰博士是共通第一作者。相信随着方法学的不断突破,人们对于菌群的研究和认知也将被拓展到新的高度。
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Science [IF:63.714]

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

菌株分辨率的高通量、单微生物基因组学,应用于人类肠道微生物组

10.1126/science.abm1483

06-02, Article

Abstract & Authors:展开

Abstract:收起
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.

First Authors:
Wenshan Zheng,Shijie Zhao

Correspondence Authors:
Peter J Lu,Eric J Alm,David A Weitz

All Authors:
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

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