Use of ‘EzTaxon’ for Naming convention
[Link].- I Microbiology
Microbial Systematics
Presented by:
Miss Vidya Vijaykumar Sonalkar
[Link]. Microbiology
CSIR NET
In bioinformatics, the EzTaxon database is a web-based tool for the identification of prokaryotes based on 16S
ribosomal RNA gene sequences.
EzTaxon is an open access database that is produced and maintained by ChunLab, Inc
The EzTaxon database contains sequences of type strains of prokaryotic species with validly published names.
Although EzTaxon is mainly used for the routine identification of prokaryotic isolates, sequences from
uncultured taxa were not included.
Thus in 2012, EzTaxon was extended to include uncultured prokaryotes and the name of the database was
changed to EzTaxon-e
Naming convention
Taxa names included in EzTaxon-e represent groups of uncultured sequences found in public domain databases.
The names included in EzTaxon-e have no standing in formal nomenclature but they were created to help in the
comparison of microbial communities and diversity in nature.
•New names found in EzTaxon-e are formed by adding special suffixes to Genbank sequence 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. SAR11, the famous marine inhabitant, is labeled
as SAR11(order), and further divided into 4 families (SAR11-1_f to SAR11-4_f).
•Based on 16S rRNA sequence phylogeny, some obviously misclassified species have been renamed using
special suffixes. For example, Bacteroides pectinophilus is not an authentic member of the genus Bacteroides.
However, it may represent a novel genus in the family Lachnospiraceae. Therefore, in the EzTaxon-e database,
Bacteroides pectinophilus is placed under a tentatively named new genus Bacteroides_g1.
•Sequences and tentative taxa that start with "4P" are products of the Roche 454 GS FLX
Titanium system.
•It is undisputed that information held in 16S rRNA gene sequences has played a vital role in microbiology
(Rossello´- Mora & Amann, 2001) and that it can be utilized in many ways in various disciplines, notably
taxonomy and ecology
•. Pairwise nucleotide similarity values of 16S rRNA gene sequences have been used routinely for the delineation
of prokaryotic species (Stackebrandt & Goebel, 1994) and have been widely accepted.
When a 16S rRNA gene sequence is applied for the identification of prokaryotic isolates, the general process
includes:
(i) similarity search against public domain nucleotide databases,
(ii) retrieval of sequences for type strains with validly published names,
(iii) calculation of pairwise nucleotide similarity values between sequences of the isolate and phylogenetically
neighbouring type strains and
(iv) phylogenetic analysis.
This process requires expertise in prokaryotic taxonomy and can be complicated and labour-intensive, as public
databases have been flooded with sequences of non-type strains including environmental clones and may
contain erroneous and mislabelled sequences. Furthermore, there are no curated databases for 16S rRNA gene
sequences of type strains of prokaryotic species
EzTaxon was successfully developed to include the collection of all reference sequences, and to provide various
functions, including a similarity search engine, calculation of pairwise similarity, multiple sequence alignment
and phylogenetic treeing algorithms at the server side.
This would allow users in places where only poor computing facilities are available to carry out most of the
necessary bioinformatic analyses of 16S rRNA gene sequences. It could also be useful in various levels of
classes for educational purposes.
