Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu.
Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu.
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具有全长 16S rRNA 序列和 Emu 的微生物群落分析方案。
DOI：
10.1002/cpz1.978
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Treangen,ToddJ
中科院分区：
文献类型：
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作者：
Curry,KristenD;Soriano,Sirena;Nute,MichaelG;Villapol,Sonia;Dilthey,Alexander;Treangen,ToddJ
16S rRNA靶向扩增子测序是阐明微生物群落组成的既定标准。虽然高通量短读段测序由于其有限的读段长度只能引出16S rRNA基因的一部分，但第三代测序可以完整地读取16S rRNA基因，从而提供更精确的分类学分类。在这里，我们提出了一个使用Oxford Nanopore Technologies（ONT）生成全长16S rRNA序列的方案，并使用Emu生成微生物群落谱。我们选择Emu来分析ONT序列，因为它利用来自整个社区的信息来克服由于参考数据库不完整和硬件限制而导致的错误，最终获得物种水平的分辨率。该管道通过利用真实的长读数ONT测序和定制软件来精确表征微生物群落，为表征微生物组组成提供了低成本的解决方案。© 2024 Wiley Periodicals LLC.基本方案：Emu微生物群落分析支持方案1：Oxford Nanopore Technologies测序平台的全长16S rRNA微生物序列支持方案2：构建Emu的自定义参考数据库
16S rRNA targeted amplicon sequencing is an established standard for elucidating microbial community composition. While high‐throughput short‐read sequencing can elicit only a portion of the 16S rRNA gene due to their limited read length, third generation sequencing can read the 16S rRNA gene in its entirety and thus provide more precise taxonomic classification. Here, we present a protocol for generating full‐length 16S rRNA sequences with Oxford Nanopore Technologies (ONT) and a microbial community profile with Emu. We select Emu for analyzing ONT sequences as it leverages information from the entire community to overcome errors due to incomplete reference databases and hardware limitations to ultimately obtain species‐level resolution. This pipeline provides a low‐cost solution for characterizing microbiome composition by exploiting real‐time, long‐read ONT sequencing and tailored software for accurate characterization of microbial communities. © 2024 Wiley Periodicals LLC.Basic Protocol: Microbial community profiling with EmuSupport Protocol 1: Full‐length 16S rRNA microbial sequences with Oxford Nanopore Technologies sequencing platformSupport Protocol 2: Building a custom reference database for Emu