In this post genomic era, accurate bacterial classification is challenging, especially at the species level, due to the increased number of reference sequences and low resolutions of currently used methods. For example, the most widely used 16S rRNA sequencing can identify only bacterial species at the genus level but not at the species levels. Advances in next generation sequencing technologies have greatly facilitated whole genome sequencing for bacterial species can be completed in a single day at low cost. Although many genome sequence data sets are accumulating, transforming them into useful information and knowledge remains challenging. In sequence based technologies, polymerase chain reaction, microarrays and metagenomics are widely used for the identification of complex microbial communities in many environments. Molecular based technologies are mainly target conserved barcoding regions or key functional genes. However, these molecular based technologies are not suitable for identifying a bacterium at species or strain level.