16S rDNA sequence analysis is a standard method in bacterial taxonomy and identification, and is based on the detection of sequence differences (polymorphisms) in the hypervariable regions of the 16S rRNA gene which is present in all bacteria. An unknown isolate can be identified by comparing the similarity of its 16S rDNA sequence with 16S rDNA sequences of strains with known taxonomic identity that are contained in public databases. However, results of similarity searches may be compromised by the quality of publicly available sequences (e.g. NCBI), which are often not validated or guaranteed, and/or the fact that many sequences from uncultured or unnamed organisms are present.
In practice, for the reliable identification of an unknown bacterial isolate, comparison with sequences of type strains with validly published prokaryotic names and taxonomically relevant groups (like representatives of uncultured phylotypes) is needed. The EZ Taxon database (http://www.ezbiocloud.net/eztaxon) takes this into account and offers a straightforward and faster alternative for conventional similarity comparisons.
At BCCM/LMG, identification using 16S rDNA sequence analysis based on the EZ Taxon database is offered as a customer service to customers and generates results at family/genus (potentially up to species) level.
Additionally, an in-depth and comprehensive phylogenetic study based on 16S rDNA sequence comparisons in BioNumerics v7.0 can be requested as a service from BCCM/LMG, e.g. in case of the description of a novel species.
The service report provided to customers will include a list of most closely related species based on sequence similarities and a scientific conclusion on the identity of the isolates provided. In case a phylogenetic study is requested, the report will also include a similarity matrix and a phylogenetic tree.
Literature
Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y.S., Lee, J.H., Yi, H., Won, S.,
Chun, J. (2012). Introducing EzTaxon: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716–721. doi: 10.1099/ijs.0.038075-0