Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
J Microbiol Methods. 2013 Dec;95(3):401-14. doi: 10.1016/j.mimet.2013.08.011. Epub 2013 Sep 9.
High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is therefore becoming more widely used to study whole communities of prokaryotes in many niches. This review discusses these techniques, including nucleic acid extraction from different environments, sample preparation and high-throughput sequencing platforms. We also discuss commonly used and recently developed bioinformatic tools applied to microbiomes, including analyzing amplicon sequences, metagenome shotgun sequences and metatranscriptome sequences. This field is relatively new and rapidly evolving, thus we hope that this review will provide a baseline for understanding these methods of microbiome analyses. Additionally, we seek to stimulate others to solve the many problems that still exist with the sensitivity, specificity and interpretation of high throughput microbiome sequence analysis.
高通量测序技术在质量、速度和成本方面都在迅速提高。因此，它在越来越多的领域中被广泛用于研究各种生境中的原核生物群落。本文综述了这些技术，包括从不同环境中提取核酸、样品制备和高通量测序平台。我们还讨论了常用于微生物组学的生物信息学工具，包括分析扩增子序列、宏基因组鸟枪法序列和宏转录组序列。这个领域相对较新且发展迅速，因此我们希望这篇综述能为理解这些微生物组分析方法提供一个基础。此外，我们希望能激发其他人解决高通量微生物组序列分析在灵敏度、特异性和解释方面仍然存在的许多问题。
