基于Illumina和Oxford Nanopore扩增子测序的16S rRNA基因对标细菌分类分配方法

IF 3.2 Q3 MICROBIOLOGY
International Journal of Microbiology Pub Date : 2025-08-13 eCollection Date: 2025-01-01 DOI:10.1155/ijm/7563096
Carmen Hoffbeck, Danielle M R L Middleton, Nicola J Nelson, Michael W Taylor
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引用次数: 0

摘要

研究生态系统或动物的微生物群落可能涉及一系列方法,包括测序技术、生物信息学软件和分类数据库。研究人员可以利用Illumina MiSeq上的短读测序或Oxford Nanopore等平台上的长读测序来获得不同的研究结果,例如,利用Nanopore增强对物种或菌株水平上的微生物的识别。然而,这些技术之间的可重复性并没有得到很好的研究,而用于将读取处理成微生物分类群的技术也可能导致不同的分类分配。在这项研究中,我们分析了一个现有的、真实世界的数据集,该数据集使用Illumina测序和SILVA数据库分析进行了低属水平鉴定,并在相同的样品上与Nanopore测序进行了比较。我们将其与每种测序技术的多种生物信息学方法和分类数据库配对,以比较门和属水平的分配,并使用模拟群落来确定哪种测序技术,生物信息学方法和分类数据库的组合提供最准确的分类。我们发现,使用生物信息学方法或分类数据库处理的纳米孔读取在模拟群落分配方面比任何与Illumina结合的技术都具有更高的准确性。我们还发现,分配给真实世界数据库的前10个属在技术组合上存在很大差异,并且与生物信息学方法或测序技术相比,分类学数据库的差异更大。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.

Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.

Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.

Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.

Research investigating the microbial community of an ecosystem or animal can involve a range of methodologies, including sequencing technology, bioinformatic software and taxonomy database. Researchers may utilise short-read sequencing on Illumina MiSeq or long-read sequencing on platforms like Oxford Nanopore to obtain different research outcomes, for example, enhanced identification of microbes at species or strain level with Nanopore. However, replicability across these techniques is not well studied, while the technique used to process reads into microbial taxa may also result in different taxonomy assignments. In this study, we analyse an existing, real-world dataset which had low genus-level identification with Illumina sequencing and analysis with the SILVA database and compare sequencing with Nanopore on the same samples. We pair this with multiple bioinformatic approaches and taxonomy databases for each sequencing technique to compare phylum- and genus-level assignments and use mock communities to identify which combination of sequencing technique, bioinformatic approach and taxonomy database provides the most accurate taxonomy. We found that Nanopore reads processed with either utilised bioinformatic approach or taxonomy database provided higher accuracy in the assignment of a mock community than any technique combination with Illumina. We also found that the Top 10 genera assigned to a real-world database were substantially different across technique combinations and varied more by taxonomy database than either bioinformatic approach or sequencing technology.

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来源期刊
CiteScore
7.90
自引率
0.00%
发文量
57
审稿时长
13 weeks
期刊介绍: International Journal of Microbiology is a peer-reviewed, Open Access journal that publishes original research articles, review articles, and clinical studies on microorganisms and their interaction with hosts and the environment. The journal covers all microbes, including bacteria, fungi, viruses, archaea, and protozoa. Basic science will be considered, as well as medical and applied research.
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