Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

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/.

Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest

“…In order to determine the confidence levels for the branches, bootstrap analysis with 1,000 replications was conducted (Felsenstein 1985). The strain DCY84 T sequence obtained was compared with those in public databases by using the EzTaxon-e server (http:// eztaxon-e.ezbiocloud.net/; Kim et al 2012) and NCBI database (http://blast.ncbi.nlm.nih.gov/Blast. cgi; Johnson et al 2008).…”

Planktonic bacterial community composition of an extremely shallow soda pond during a phytoplankton bloom revealed by cultivation and molecular cloning

“…The obtained sequences were aligned in NCBI (National Centre for Biotechnology Information) (www.ncbi.nlm.nih.gov) using the BLAST (Basic Local Alignment and Search Tool) program (Altschul et al 1997) and by EzTaxon-e identification service (Kim et al 2012) against the database of type strains with validly published prokaryotic names.…”

Bio-Prospecting Laccases in the Bacterial Diversity of Activated Sludge From Pulp and Paper Industry

“…Further, sequence reads were assembled and taxonomic assignment of each read was conducted using the EzTaxon-e database, which contains representative phylotypes of cultured and uncultured sequences in the GenBank database [20]. The operational taxonomic units (OTUs) were defined with the CD-HIT program [21].…”