Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted (“shotgun”) sequencing of all (“meta”) microbial genomes (“genomic”) present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

中文翻译：

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使用高通量测序技术进行微生物群落分析：微生物学家入门指南

从深海到人体生态位的各种环境中存在的微生物群落在复杂的生态系统和人类健康中发挥着重要作用。表征它们的结构和功能多样性是必不可少的，并且许多方法，例如显微镜观察，DNA指纹识别和基于PCR的标记基因分析，已成功地用于鉴定微生物。自从DNA测序技术得到革命性的改进以来，无需事先培养即可直接从整个环境社区进行基因组DNA的直接和高通量分析已成为主流方法，克服了传统方法的局限性。这里，我们首先简要回顾一下环境DNA分析应用的历史，重点是分析微生物群落的分类学组成和功能潜力。为此，我们旨在介绍the弹枪宏基因组测序（SMS）方法，该方法用于样品中所有（“元”）微生物基因组（“基因组”）的非靶向（“ shot弹枪”）测序。进行SMS数据分析在计算机上使用各种软件程序；但是，计算机分析通常被认为是湿实验室微生物学家的负担。因此，在这篇综述中，我们介绍了不熟悉计算机模拟分析以及基本和实用的SMS数据分析协议的微生物学家。该协议涵盖了数据预处理，分类分析，功能注释和可视化方面的SMS分析的所有生物信息学过程。