ABSTRACT The human oral cavity is home to one of the most diverse, dynamic and complex collections of microbes (the ‘oral microbiota’) with an estimated 700–1,000 different microbial species inhabiting a variety of ecological niches, such as the teeth, tongue, gums and saliva. Despite decades of research, much is still unknown of the functions and activities of the oral microbiota as many species, particularly those discovered by culture-independent (molecular) techniques, are yet to be cultivated. The past decade has seen the introduction of so-called next-generation DNA sequencing (NGS) technologies which can generate unprecedented amounts of DNA sequence data quickly and reliably. NGS has revolutionised the study of oral microbiota by allowing microbial community profiling in health and disease. Furthermore, NGS facilitates the cost-effective sequencing of individual microbial genomes. Over the past 10 years, our research groups have collaborated on a variety of NGS projects involving whole-genome sequencing of a variety of oral and non-oral bacteria, and oral microbiota profiling in health and disease (severe dental caries and periodontal disease). This paper aims to provide an overview of the NGS technologies we have used and the bioinformatic tools available to analyse NGS-scale datasets, and to highlight some of our NGS achievements.

中文翻译：

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约翰沃尔什爵士研究所口腔微生物的下一代 DNA 测序：技术、工具和成就

摘要 人类口腔是最多样化、动态和复杂的微生物群之一（“口腔微生物群”），估计有 700-1,000 种不同的微生物物种栖息在各种生态位，如牙齿、舌头、牙龈和唾液。尽管进行了数十年的研究，但口腔微生物群的功能和活动仍有很多未知，因为许多物种，尤其是那些通过独立培养（分子）技术发现的物种，还有待培养。在过去的十年中，引入了所谓的下一代 DNA 测序 (NGS) 技术，该技术可以快速可靠地生成前所未有的大量 DNA 序列数据。NGS 通过对健康和疾病中的微生物群落进行分析，彻底改变了口腔微生物群的研究。此外，NGS 有助于对单个微生物基因组进行经济高效的测序。在过去的 10 年中，我们的研究小组合作开展了各种 NGS 项目，涉及各种口腔和非口腔细菌的全基因组测序，以及健康和疾病（严重龋齿和牙周病）中的口腔微生物群分析。本文旨在概述我们使用的 NGS 技术和可用于分析 NGS 规模数据集的生物信息学工具，并重点介绍我们的一些 NGS 成就。