Institute Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
Norwegian University of Life Sciences (NMBU), Ås, Norway.
BMC Res Notes. 2021 Feb 2;14(1):42. doi: 10.1186/s13104-021-05457-3.
Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.
With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in > 1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.
目前，海水环境中大部分不可培养的微生物尚未被发现，而纳米孔测序技术为克服识别海洋微生物组的基因组和复杂组成的挑战性任务提供了一种解决方案。本研究评估了牛津纳米孔技术（ONT）测序在表征来自多个地点海水微生物多样性中的应用。我们比较了两个不同地点和时间点的环境样本中微生物物种多样性。
仅使用三个 ONT 流动池，我们就能够鉴定出数千种生物体，包括噬菌体，其中很大一部分达到了种水平。通过 Flye 可以对环境样本进行基因组组装。在某些情况下，这会产生超过 1 Mbp 的 contigs，而在一个 Thioglobus singularis 物种的特殊情况下，甚至产生了一个近乎完整的基因组。k-mer 分析表明，很大一部分数据代表了尚未在数据库中记录的近缘种。这些结果表明，我们的方法适用于可扩展的基因组研究，如监测海洋生物多样性，并为生物多样性教育提供了一个新的平台。
