Chappidi Sruthi, Villa Erika C, Cantarel Brandi L
Department of Computer Science, University of Texas at Dallas, Richardson, Texas.
Bioinformatics Core Facility, Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas.
Curr Protoc Bioinformatics. 2019 Sep;67(1):e83. doi: 10.1002/cpbi.83.
The 16S ribosomal RNA (rRNA) gene is one of the scaffolding molecules of the prokaryotic ribosome. Because this gene is slow to evolve and has very well conserved regions, this gene is used to reconstruct phylogenies in prokaryotes. Universal primers can be used to amplify the gene in prokaryotes including bacteria and archaea. To determine the microbial composition in microbial communities using high-throughput short-read sequencing techniques, primers are designed to span two or three of the nine variable regions of the gene. Mothur, developed in 2009, is a suite of tools to study the composition and structure of bacterial communities. This package is freely available from the developers (https://www.mothur.org). This protocol will show how to (1) perform preprocessing of sequences to remove errors, (2) perform operational taxonomic unit (OTU) analysis to determine alpha and beta diversity, and (3) determine the taxonomic profile of OTUs and the environmental sample. © 2019 The Authors.
16S核糖体RNA（rRNA）基因是原核生物核糖体的支架分子之一。由于该基因进化缓慢且具有高度保守的区域，因此被用于重建原核生物的系统发育。通用引物可用于扩增包括细菌和古菌在内的原核生物中的该基因。为了使用高通量短读长测序技术确定微生物群落中的微生物组成，引物被设计为跨越该基因九个可变区域中的两个或三个。Mothur于2009年开发，是一套用于研究细菌群落组成和结构的工具。该软件包可从开发者处免费获取（https://www.mothur.org）。本方案将展示如何（1）对序列进行预处理以去除错误，（2）进行操作分类单元（OTU）分析以确定α和β多样性，以及（3）确定OTU的分类概况和环境样本。© 2019作者。
