Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.
Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.
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DOI：
10.1038/s41467-020-20199-9
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发表时间：
2021-01-04
影响因子：
16.6
通讯作者：
Okazaki Y
中科院分区：
文献类型：
--
作者：
Yahara K;Suzuki M;Hirabayashi A;Suda W;Hattori M;Suzuki Y;Okazaki Y
噬菌体（噬菌体）或细菌病毒在全世界范围内非常多样化且丰富，包括作为人类微生物组的一部分。尽管一些宏基因组研究关注口腔噬菌体，但它们依赖于短读长测序。在这里，我们使用 PromethION 对人类唾液进行了长期的宏基因组研究。我们的分析整合了每个样本 >30 Gb 的 PromethION 和 HiSeq 数据以及低人类 DNA 污染，识别了数百个病毒重叠群；分别有 0-43.8% 和 12.5-56.3% 的可信预测噬菌体和原噬菌体与之前报道的不聚类。我们的分析证明了增强的支架，以及将原噬菌体置于其宿主基因组环境中并实现其分类学分类的能力。我们的分析还确定了链球菌噬菌体/原噬菌体群和九个巨型噬菌体/原噬菌体。 86% 的噬菌体/原噬菌体组和 67% 的巨型噬菌体/原噬菌体含有抗菌素耐药性基因的远程同源物。噬菌体/原噬菌体的泛基因组分析显示出显着的多样性，分别鉴定出 0.3% 和 86.4% 的基因为核心基因和单基因。此外，我们的研究表明，人类唾液中存在的口腔噬菌体面临选择性压力，以逃避 CRISPR 免疫。我们的研究证明了利用 PromethION 进行长读宏基因组学揭示噬菌体及其与宿主细菌相互作用的能力。在这里，作者使用 PromethION（一种最近开发的高通量纳米孔测序仪）通过长读霰弹枪宏基因组学分析了 4 名健康个体的口腔噬菌体，并发现了具有增强支架的潜在新候选噬菌体及其与宿主细菌的相互作用。
Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conduct a long-read metagenomic study of human saliva using PromethION. Our analyses, which integrate both PromethION and HiSeq data of >30 Gb per sample with low human DNA contamination, identify hundreds of viral contigs; 0–43.8% and 12.5–56.3% of the confidently predicted phages and prophages, respectively, do not cluster with those reported previously. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria. Here, the authors profile the oral phageome of 4 healthy individuals via longread shotgun metagenomics using PromethION, a recently developed highthroughput nanopore sequencer, and uncover potential new candidate phages with enhanced scaffolding and their interaction with host bacteria.
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