Introducing EzTaxon-e

A prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species

Ok Sun Kim, Yong Joon Cho, Kihyun Lee, Seok Hwan Yoon, Mincheol Kim, Hyunsoo Na, Sang Cheol Park, Yoon Seong Jeon, Jae Hak Lee, Hana Yi, Sungho Won, Jongsik Chun

Research output: Contribution to journalArticle

4011 Citations (Scopus)

Abstract

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/.

Original languageEnglish
Pages (from-to)716-721
Number of pages6
JournalInternational Journal of Systematic and Evolutionary Microbiology
Volume62
Issue numberPART 3
DOIs
Publication statusPublished - 2012 Mar 1
Externally publishedYes

Fingerprint

rRNA Genes
Genes
ribosomal RNA
Databases
nucleotide sequences
gene
prokaryote
prokaryotic cells
Identification (control systems)
Sequence Alignment
sequence alignment
phylotype
Names
taxonomy
phylogenetics
Communication
phylogeny
genes

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Introducing EzTaxon-e : A prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species. / Kim, Ok Sun; Cho, Yong Joon; Lee, Kihyun; Yoon, Seok Hwan; Kim, Mincheol; Na, Hyunsoo; Park, Sang Cheol; Jeon, Yoon Seong; Lee, Jae Hak; Yi, Hana; Won, Sungho; Chun, Jongsik.

In: International Journal of Systematic and Evolutionary Microbiology, Vol. 62, No. PART 3, 01.03.2012, p. 716-721.

Research output: Contribution to journalArticle

Kim, Ok Sun ; Cho, Yong Joon ; Lee, Kihyun ; Yoon, Seok Hwan ; Kim, Mincheol ; Na, Hyunsoo ; Park, Sang Cheol ; Jeon, Yoon Seong ; Lee, Jae Hak ; Yi, Hana ; Won, Sungho ; Chun, Jongsik. / Introducing EzTaxon-e : A prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species. In: International Journal of Systematic and Evolutionary Microbiology. 2012 ; Vol. 62, No. PART 3. pp. 716-721.
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