Kristen D. Curry, Sirena Soriano, Michael G. Nute, Sonia Villapol, Alexander Dilthey, Todd J. Treangen
{"title":"利用全长 16S rRNA 序列和 Emu 进行微生物群落分析的协议","authors":"Kristen D. Curry, Sirena Soriano, Michael G. Nute, Sonia Villapol, Alexander Dilthey, Todd J. Treangen","doi":"10.1002/cpz1.978","DOIUrl":null,"url":null,"abstract":"<p>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.</p><p><b>Basic Protocol</b>: Microbial community profiling with Emu</p><p><b>Support Protocol 1</b>: Full-length 16S rRNA microbial sequences with Oxford Nanopore Technologies sequencing platform</p><p><b>Support Protocol 2</b>: Building a custom reference database for Emu</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"4 3","pages":""},"PeriodicalIF":2.2000,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu\",\"authors\":\"Kristen D. Curry, Sirena Soriano, Michael G. Nute, Sonia Villapol, Alexander Dilthey, Todd J. Treangen\",\"doi\":\"10.1002/cpz1.978\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>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.</p><p><b>Basic Protocol</b>: Microbial community profiling with Emu</p><p><b>Support Protocol 1</b>: Full-length 16S rRNA microbial sequences with Oxford Nanopore Technologies sequencing platform</p><p><b>Support Protocol 2</b>: Building a custom reference database for Emu</p>\",\"PeriodicalId\":93970,\"journal\":{\"name\":\"Current protocols\",\"volume\":\"4 3\",\"pages\":\"\"},\"PeriodicalIF\":2.2000,\"publicationDate\":\"2024-03-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Current protocols\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/cpz1.978\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current protocols","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpz1.978","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
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