Complete, closed bacterial genomes from microbiomes using nanopore sequencing
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
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DOI：
10.1038/s41587-020-0422-6
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发表时间：
2020-02-10
影响因子：
46.9
通讯作者：
Bhatt, Ami S.
中科院分区：
文献类型：
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作者：
Moss, Eli L.;Maghini, Dylan G.;Bhatt, Ami S.
微生物基因组可以从短读段测序数据组装，但是这些宏基因组组装的基因组的组装邻接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。我们应用纳米孔测序和我们的工作流程，命名为车床，它结合了长读组装和短读纠错，从复杂的微生物组组装封闭的细菌基因组。我们用12种细菌的合成混合物验证了我们的方法。七个基因组完全组装成单个重叠群，三个基因组组装成四个或更少的重叠群。接下来，我们使用我们的方法分析了来自13个人类粪便样本的宏基因组学数据。我们组装了20个环状基因组，包括普雷沃氏菌和一个候选的Cibibibiotella sp.的基因组。尽管与其他测序和组装方法相比，核苷酸的准确性降低，我们的方法提高了组装的连续性，允许调查重复元件在微生物功能和adaptation.Nanopore-metagenomics工作流程中的作用，使完整的，封闭的细菌基因组从人类粪便样品组装。
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.Nanopore-metagenomics workflow enables assembly of complete, closed bacterial genomes from human stool samples.