Rajilić-Stojanović Mirjana, Smidt Hauke, de Vos Willem M
Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands.
Environ Microbiol. 2007 Sep;9(9):2125-36. doi: 10.1111/j.1462-2920.2007.01369.x.
Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
自一个多世纪前微生物学早期以来，已从人类胃肠道样本中分离并全面鉴定了400多种不同微生物物种的代表。然而，在过去十年中，基于核糖体RNA（rRNA）序列的分子生态学研究表明，培养方法只能获取胃肠道内微生物多样性的一小部分。越来越多的rRNA序列存入数据库，这就需要建立一个经过整理的数据库，以处理威胁公共数据库可用性的过度冗余问题。本文首次展示了基于培养的研究数据与小亚基（SSU）rRNA多样性分子清单的整合，提供了一个包含1000多种不同物种水平系统发育类型（系统型）的人类胃肠道微生物多样性的系统框架。这些知识对于设计高通量方法（如系统发育DNA微阵列）至关重要，该方法可在多个分类分辨率水平上对胃肠道微生物群进行综合分析。开发此类方法可能对深入了解健康和疾病状态下微生物群的功能起着关键作用。
