Nanopore and Illumina Sequencing Reveal Different Viral Populations from Human Gut Samples
Nanopore and Illumina Sequencing Reveal Different Viral Populations from Human Gut Samples
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Nanopore 和 Illumina 测序揭示了人类肠道样本中的不同病毒种群
DOI：
10.1101/2023.11.24.568560
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Cook R
中科院分区：
文献类型：
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作者：
Cook R
病毒元基因组学或病毒学的出现，提高了我们对全球病毒多样性的认识和理解。高通量测序技术能够探索病毒在各种环境中的生态作用、对宿主新陈代谢的贡献以及病毒对包括人类肠道微生物组在内的各种环境的影响。然而，细菌元基因组研究往往具有优势。长读测序等先进技术的采用有可能在提炼病毒组和元基因组学方面产生变革。在这里，我们通过比较Illumina Short-Read和牛津纳米孔技术(ONT)的Long-Read测序技术和不同的组装策略从人类粪便样本中恢复病毒基因组，来检验长读测序和混合测序的有效性。我们的发现表明，如果要选择单一的测序技术进行病毒体分析，Illumina更可取，因为它具有恢复完全解析的病毒基因组和将错误基因组降至最低的优越能力。虽然ONT组件在恢复病毒多样性方面是有效的，但与投入要求和扩增必要性相关的挑战使其作为独立解决方案不太理想。然而，使用一种组合的混合方法使得能够在样本中获得更真实的病毒多样性表示。
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.