Specialized High-Quality 16S Ribosomal RNA Gene Databases for Identification of Bacterial Taxonomic Groups: a review

Recent accumulation of the bacterial 16S and 23S rRNA gene sequences in the public GenBank databases obtained from the wide use of the Polymerase Chain Reaction (PCR) and the Next Generation Sequencing (NGS) applications has led the specialists in the fields of microbiology and bioinformatics to provide specific and reliable databases for storing, retrieving and aligning bacterial ribosomal gene sequences. In our review, we have provided a comprehensive description of gene databases with an emphasis on the most specialized and high quality rRNA gene databases. These databases are freely accessible and widely used for all specialist users for accurate bacterial genera and species identification from different sources. rRNA genes, platforms, internet addresses and references of each gene specialized database were outlined. The Silva, EzTaxon-e and BIBI have been shown to be the most confident and reliable specialized rRNA gene databases. These databases contain the semi fully high-quality ribosomal gene sequences along with some house-keeping and uncultured gene sequences in case of EzTaxon-e.