Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
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DOI：
10.1038/s41587-019-0191-2
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发表时间：
2019-08-01
影响因子：
46.9
通讯作者：
Nagarajan, Niranjan
中科院分区：
文献类型：
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作者：
Bertrand, Denis;Shaw, Jim;Nagarajan, Niranjan
高通量宏基因组测序使微生物群落的特征分析成为可能。然而，现有的方法并非旨在结合短读长和长读长技术的测序数据。我们提出了一种名为OPERA - MS的混合宏基因组组装程序，它将基于组装的宏基因组聚类与重复识别、精确的支架构建相结合，以准确组装复杂的微生物群落。通过使用定义明确的体外和虚拟肠道微生物群落进行评估，结果表明OPERA - MS组装宏基因组的碱基对准确性高于长读长技术（>5倍；Canu），连续性高于短读长技术（类似于10倍NGA50；MEGAHIT、IDBA - UD、metaSPAdes），并且组装错误少于非宏基因组混合组装程序（2倍；hybridSPAdes）。在存在同一物种的多个基因组的情况下，OPERA - MS可提供菌株分辨的组装，为稀有物种（<1%）提供高质量的参考基因组，其长读长覆盖度类似于9倍，并且在更高覆盖度下可提供近乎完整的基因组。我们使用OPERA - MS组装了28个接受抗生素治疗患者的肠道宏基因组，结果表明纳入长纳米孔读长可产生更连续的组装（相较于短读长组装提高200倍），包括80多个闭合的质粒或噬菌体序列以及一个新的263kbp巨型噬菌体。高质量的混合组装能够极其详细地呈现人类患者肠道耐药基因组的情况。
Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short-and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5x; Canu), higher contiguity than short-read (similar to 10x NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2x; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (< 1%) with similar to 9x long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200x improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.