Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
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DOI：
10.1099/ijs.0.038075-0
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发表时间：
2012-03-01
影响因子：
2.8
通讯作者：
Chun, Jongsik
中科院分区：
文献类型：
--
作者：
Kim, Ok-Sun;Cho, Yong-Joon;Chun, Jongsik
尽管商业上优化的鉴定系统最近取得了进展，但在许多常规微生物实验室中，细菌鉴定仍然是一项具有挑战性的任务，特别是在涉及分类上新颖的分离物的情况下。16S rRNA基因已被广泛用于这项任务，当与一个精心策划的数据库（如EzTaxon）相结合时，该数据库包含具有有效公布名称的原核物种类型菌株序列。虽然EzTaxon数据库已广泛用于原核分离物的常规鉴定，但未培养的原核生物的序列尚未被考虑。在这里，正式介绍下一代数据库EzTaxon-e。这个新的数据库不仅涵盖了正式命名系统内的物种，而且还包括可能代表自然界物种的种型。在基本局部比对搜索工具（BLAST）和两两全局序列比对的基础上，提出了一种新的评价序列完整性的客观方法。所有保存在EzTaxon-e数据库中的序列都进行了系统发育分析，这导致了一个完整的分层分类系统。由此得出结论，EzTaxon-e数据库为鉴定培养和未培养的原核生物提供了有用的分类支柱，并为经常遇到分类上新颖的分离株的微生物学家提供了有价值的交流手段。该数据库及其分析功能可在http://eztaxon-e.ezbiocloud.net/上找到。
Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (BLAST) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.