Low-depth Raw Reads of Nanopore Sequencing Enables Rapid and Accurate Bacterial Identification

IF 1 4区生物学 Q4 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Applied Biochemistry and Microbiology Pub Date : 2023-12-10 DOI:10.1134/s0003683823060042

W. Gao, H. Li, W. Hong, S. Liu, J. Li, Y. Wu, Y. Liu, X. Fan, H. Wang, M. Wang, B. Yang, T. Wang

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Abstract

The recent advent of third-generation sequencing technologies brings promise for better bacterial identification. However, the commercial applications of the current sequencing technologies are still constrained since their high cost and error rate of this sequencing technology. Thus, strategies for time-saving bacterial identification with low cost and high accuracy are urgently needed. In this study, we evaluated the performance of the Nanopore long-read sequencer and the Illumina platform alone or in combination with different data volume (0.5–80×) after assembly, to ascertain whether the incomplete genomes enable accurate bacterial identification. The results showed that the average nucleotide identity value of hybrid assembly and Illumina assembly does not change much as the amount of data increases. In addition, the ANI value reached a plateau at 5×, while the ANI values of Nanopore-only assemblies increased in the range of 5–30×. Since the assembly process was time-consuming, this study compared the accuracy of the Nanopore long-read sequencer in species identification with various sets of the reads (0.5–80×), to further confirm the minimum amount of data required for accurate bacteria identification. Without assembly, it enabled rapid and accurate bacterial identification with low coverage of Nanopore raw reads (0.5×). The results of study suggested the potential of Nanopore sequencing in rapid bacteria identification using low-depth raw reads (0.5×) without assembly, and provided data basis in developing new strategy for bacterial identification.

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纳米孔测序的低深度原始读数可实现快速准确的细菌鉴定

摘要最近出现的第三代测序技术为更好地鉴定细菌带来了希望。然而，由于目前的测序技术成本高、错误率高，其商业应用仍然受到限制。因此，我们迫切需要低成本、高准确性、省时的细菌鉴定策略。在本研究中，我们评估了 Nanopore 长读数测序仪和 Illumina 平台在组装后单独或组合使用不同数据量（0.5-80×）的性能，以确定不完整基因组是否能准确鉴定细菌。结果表明，随着数据量的增加，混合组装和 Illumina 组装的平均核苷酸同一性值变化不大。此外，平均核苷酸同一性值在 5 倍时达到了高点，而纯 Nanopore 组装的平均核苷酸同一性值则在 5-30 倍的范围内增加。由于组装过程耗时较长，本研究比较了 Nanopore 长读数测序仪在不同读数集（0.5-80×）下进行物种鉴定的准确性，以进一步确认准确鉴定细菌所需的最小数据量。在不进行组装的情况下，利用低覆盖率的 Nanopore 原始读数（0.5×）可以快速准确地鉴定细菌。研究结果表明，纳米孔测序技术在使用低深度原始读数（0.5×）（无需组装）快速鉴定细菌方面具有潜力，并为开发细菌鉴定新策略提供了数据基础。

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来源期刊

Applied Biochemistry and Microbiology 生物-生物工程与应用微生物

CiteScore

1.70

自引率

12.50%

发文量

审稿时长

6-12 weeks

期刊介绍： Applied Biochemistry and Microbiology is an international peer reviewed journal that publishes original articles on biochemistry and microbiology that have or may have practical applications. The studies include: enzymes and mechanisms of enzymatic reactions, biosynthesis of low and high molecular physiologically active compounds; the studies of their structure and properties; biogenesis and pathways of their regulation; metabolism of producers of biologically active compounds, biocatalysis in organic synthesis, applied genetics of microorganisms, applied enzymology; protein and metabolic engineering, biochemical bases of phytoimmunity, applied aspects of biochemical and immunochemical analysis; biodegradation of xenobiotics; biosensors; biomedical research (without clinical studies). Along with experimental works, the journal publishes descriptions of novel research techniques and reviews on selected topics.