43,055 prokaryotic 16S rRNA gene sequences in the database, as of March 1, 2013 If you use this service for your study, please cite the paper by Kim et al. (2012). [More]
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- Please join Bergey’s International Society for Microbial Systematics. (May 9, 2013)
Dear Colleague,
We write to invite you, your colleagues and your students to consider joining the Bergey’s International Society for Microbial Systematics (BISMiS).
The purpose of the society is to promote excellent research in microbial systematics as well as enhance global communication among taxonomists who study the Bacteria and Archaea. The society also serves internationally as an advocate for research efforts on microbial systematics and diversity. In the light of molecular methods (16S, next- generation sequencing methods including genome analysis) tremendous advances in our understanding of microbial evolution and taxonomy have been made. However this in itself has led to questions on the future direction of modern day systematics that embraces taxonomic concepts and practices. It is essential that this debate is open to as many participants as possible and membership of BISMiS ensures your voice is heard.
Publications: The Microbial Taxonomist, the newsletter of Bergey's Manual Trust is a valuable resource for up-to-date information on matters relating to taxonomy and Bergey’s Manual. It is free to everyone, and members of BISMiS are automatically subscribed. The Bulletin of BISMiS is published twice yearly and sent to members immediately upon publication. It is then released for open access 6 months following publication. The Bulletin focuses on invited opinion articles, review articles, educational articles on methodologies, and invited autobiographies and biographies. I think you will agree, articles to date have been of remarkably quality and diversity and have stimulated much discussion amongst our membership.
Meetings: BISMiS sponsors meeting of interest to microbial systematics. The first meeting was entitled “Microbial Systematics: Concepts, Practices and Recent Advances” and was held at the Friendship Hotel Beijing, China, on 19-23 May 2011. The next meeting is planned for Edinburgh in April 2014.
The subsequent paper (Kim et al. 2012) describing the next generation EzTaxon-e database is also widely accepted and getting more citations (33).
Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. & Lim, Y. W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259-2261.
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-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716–721.
- EzTaxon identification service is recommended for the clinical laboratories. (October 5, 2012)
Park et al. (2012) evaluated currently available web-based databases for 16S rRNA-based bacterial identification in the cases that other conventional methods gave incomplete, conflicting and unworkable results.
They recommend the combination of EzTaxon and GenBank in the routine identification of clinical bacterial strains.
They used old EzTaxon database, and the current version, EzTaxon-e database, has more sequences to cover broader range of bacterial species which may be isolated in clinical diagnostic laboratories.
The work has been published in the Journal of Clinical Microbiology.
Park, K. S., Ki, C. S., Kang, C. I., Kim, Y. J., Chung, D. R., Peck, K. R., Song, J. H. & Lee, N. Y. (2012). Evaluation of the GenBank, EzTaxon, and BIBI services for molecular identification of clinical blood culture isolates that were unidentifiable or misidentified by conventional methods. J Clin Microbiol 50, 1792-1795.
- New algorithm applied for EzTaxon identification service. (September 10, 2012)
Identification in the EzTaxon server involves two different steps:
(i) initial search step to find the potentially closely related sequences and
(ii) pairwise alignment step to calculate sequence similarity values between query sequence and sequences identified by the step (i).
In the previous algorithm, we used both BLASTN and megaBLAST programs with whole (full length) query sequence in the initial search step. In this new algorithm, we used BLASTN searches with four different query sequences. Firstly, the closest sequences in the database are identified using whole (full length) query sequence as a query in BLASTN search. The query sequence is then divided into three pieces with equal length, and each is used as a query sequence for BLASTN search. Top hits from these four search operations are combined and subjected to pairwise sequence alignment (Myers & Miller, 1988) with the original full length query sequence. Using this new algorithm, one can find the shorter target sequences in the database. We recommend that top 30 hits are saved and used for pairwise sequence similarity calculation. Since top hits are combined from four different BLASTN searches, the final results should contain 30 to 120 hits (if top 30 hits option was chosen).
Introducing EzTaxon-e database:
The EzTaxon-e database is an extension of the original EzTaxon database (Chun et al., 2007) which has been cited over 1,160 times. It now contains comprehensive 16S rRNA gene sequences of taxa with valid names as well as sequences of uncultured taxa.
The EzTaxon-e database is an extended version of EzTaxon database, and now contains:
16S rRNA gene sequences of type strains of species with validly described names
16S rRNA gene sequences of candidatus taxa
Selected representative 16S rRNA gene sequences from uncultured prokaryotes. We carried out extensive phylogenetic analysis on uncultured sequences from public domain database and identified representatives by using 3% sequence similarity as a species boundary. Thus, these sequences can serve types of the tentative yet-uncultivated species.
Complete hierarchical taxonomic structure (from phylum rank to species rank) of the domain Bacteria and Archaea.
Naming convention of EzTaxon-e:
In addition to the formally described names, the names included in the EzTaxon-e database represent groups of uncultured sequences found in public domain databases. These tentative names have no standing in formal nomenclature. We propose this new hierarchical classification scheme to help comparison of microbial community and diversity in nature. We do not intend to propose any formal taxonomic changes whatsoever from this new classification scheme.
The EzTaxon-e database is an extended version of EzTaxon database, and now contains:
In general, new names are formed by adding special suffixes to the Genbank accession numbers of sequences (e.g. AB177171_s -> species of which the sequence entry AB177171 serves type; AB177171_g -> genus; AB177171_f -> family; AB177171_o -> order; AB177171_c -> class; AB177171_p -> phylum)
Well-known names have been preserved for historical reasons. For example, SAR11, the famous marine inhabitant, is labeled as SAR11(order) , and further divided into 4 families (SAR11-1_f to SAR11-4_f).
On the basis of 16S rRNA sequence phylogeny, some obviously misclassified species have been named with modification using the special suffix. For example, Bacteroides pectinophilus is not authentic member of the genus Bacteroides. However, it may represent a novel genus in the family Lachnospiraceae. So, in our scheme, Bacteroides pectinophilus is placed under a tentatively named new genus Bacteroides_g1. The most remarkable example comprises the members of the genus Clostridium which have been reassigned into more than 10 genera in this scheme. Again, our new nomenclature is not based on formal nomenclature, and only based on 16S rRNA phylogeny.
Sequences and tentative taxa with the names starting with “4P” are the products of the Roche 454 GS FLX Titanium system. These are designed to be being used until we have full length 16S rRNA sequences.
