小柯机器人

美国斯坦福大学Ami S. Bhatt研究组使用纳米孔测序从微生物组获得完整封闭细菌基因组。2020年2月10日，国际学术期刊《自然—生物技术》在线发表了这一成果。

他们应用了纳米孔测序技术，其工作流程（称为车床）结合了长片段组装和短片段纠错功能，可以从复杂的微生物组中组装封闭的细菌基因组。他们用12种细菌的合成混合物验证了他们的方法。七个基因组被完全组装成一个重叠群，三个基因组被组装成四个或更少的重叠群。接下来，他们使用该方法来分析来自13个人粪便样本的宏基因组学数据。他们组装了20个环状基因组，包括普雷沃氏杆菌和候选柠檬杆菌的基因组。尽管与其他测序和组装方法相比核苷酸准确性降低，但他们的方法提高了组装连续性，可研究重复元件在微生物功能和适应中的作用。

据悉，可以从短片段测序数据中组装微生物基因组，但是这些元基因组组装的连续性受到重复元件的限制。正确分配重复序列的基因组位置对于理解基因组结构对基因组功能的影响至关重要。

附：英文原文

Title: Complete, closed bacterial genomes from microbiomes using nanopore sequencing

Author: Eli L. Moss, Dylan G. Maghini, Ami S. Bhatt

Issue&Volume: 2020-02-10

Abstract: Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.

DOI: 10.1038/s41587-020-0422-6

Source: https://www.nature.com/articles/s41587-020-0422-6

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex