Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure–function relationships in complex environments. To compare the recovery of genomes from microorganisms and their viruses from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore Technologies (ONT) sequencing platform. Assembly and metagenome‐assembled genome (MAG) metrics for both microbes and viruses were determined from an Illumina‐only assembly, ONT‐only assembly, and a hybrid assembly approach. The hybrid approach recovered 2× more mid to high‐quality MAGs compared to the Illumina‐only approach and 4× more than the ONT‐only approach. A similar number of viral genomes were reconstructed using the hybrid and ONT methods, and both recovered nearly fourfold more viral genomes than the Illumina‐only approach. While yielding fewer MAGs, the ONT‐only approach generated MAGs with a high probability of containing rRNA genes, 3× higher than either of the other methods. Of the shared MAGs recovered from each method, the ONT‐only approach generated the longest and least fragmented MAGs, while the hybrid approach yielded the most complete. This work provides quantitative data to inform a cost–benefit analysis of the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.

中文翻译：

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包含牛津纳米孔长读本可改善复杂含水层系统中所有微生物和病毒超基因组组装的基因组。

从元基因组组装微生物和病毒基因组是一种了解复杂环境中结构与功能关系的强大且有吸引力的方法。为了比较微生物和地下水中病毒基因组的回收率，我们使用Illumina测序生成了gun弹枪的基因组，并附带了牛津纳米孔技术（ONT）测序平台的长读。微生物和病毒的组装和元基因组组装基因组（MAG）指标是通过仅Illumina组装，仅ONT组装和混合组装方法确定的。与仅使用Illumina的方法相比，混合方法可恢复2倍以上的中高品质MAG，而仅使用ONT的方法则可恢复4倍以上。使用杂交和ONT方法重建了相似数量的病毒基因组，与仅使用Illumina的方法相比，这两种方法都能恢复近四倍的病毒基因组。尽管生成的MAG较少，但仅使用ONT的方法生成的MAG包含rRNA基因的可能性很高，比其他任何一种方法高3倍。从每种方法中回收的共享MAG中，仅ONT方法生成的时间最长，碎片最少，而混合方法生成的则最完整。这项工作提供了定量数据，可以为对shot弹枪宏基因组学项目进行补充的决定提供成本效益分析，并为此进行了长期阅读，以期从环境丰富的人群中回收基因组。从每种方法中回收的共享MAG中，仅ONT方法生成的时间最长，碎片最少，而混合方法生成的则最完整。这项工作提供了定量数据，可以为对shot弹枪宏基因组学项目进行补充的决定提供成本效益分析，并为此进行了长期阅读，以期从环境丰富的人群中回收基因组。从每种方法中回收的共享MAG中，仅ONT方法生成的时间最长，碎片最少，而混合方法生成的则最完整。这项工作提供了定量数据，可以为对shot弹枪宏基因组学项目进行补充的决定提供成本效益分析，并为此进行了长期阅读，以期从环境丰富的人群中回收基因组。