Department of Computer Science, Fu Foundation School of Engineering & Applied Science, Columbia University, New York, NY, USA.
Methods Mol Biol. 2021;2243:107-122. doi: 10.1007/978-1-0716-1103-6_6.
Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome-a collection of bacteria, fungi, archaea, and viruses inhabiting an environment--is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.
微生物群落存在于各种环境中，包括人体内部和外部。由于许多微生物在实验室中无法培养，因此人们对微生物组（居住在特定环境中的细菌、真菌、古菌和病毒的集合）的了解主要来自于对组成群落的 DNA 进行测序。在这里，我们通过综述宏基因组学的三个主要研究领域——组装、群落分析和功能分析，对全基因组鸟枪法测序研究进行了介绍，该方法是一种用于描述微生物群落的普遍方法。尽管不详尽，但这些领域涵盖了宏基因组学文献的很大一部分。我们深入讨论了每个领域、全基因组鸟枪法测序所带来的挑战，以及解决每个问题的基本方法。最后，我们讨论了未来研究的有前景的领域。尽管我们的重点是人体微生物组，但讨论的方法在广泛的研究系统中都具有广泛的适用性。
