The 16S-23S rDNA internal transcribed spacer (ITS) sequence, located in the rrn operon, has been analyzed and evaluated for use in phylogenetic analysis and the detection target of bacteria. The ITS region displays a high level of diversity, being present in multiple copies and displaying variability in both length and sequence, and it carries more phylogenetic information than 16S rDNA. However, appropriately identifying ITS regions to use in analyses is challenging. To solve this problem, we analyzed the ITS regions in Vibrio parahaemolyticus and predicted the secondary structure of each analogous rrn transcript. The genomic DNA of V. parahaemolyticus contains approximately 8-14 rrns, making it more complex than the sequences of most other bacterial species. We analyzed 216 ITSs, of which 206 ITSs come from 18 complete genomes, and 10 ITSs were identified in the present study. The subunits of each ITS were distinguished by their predicted secondary structures. We propose a refined backbone model of the V. parahaemolyticus ITS that can be applied to the sequences of other bacteria. The backbone includes C, V, tDNA and linker blocks. These blocks, which may represent true functional units, may be used as potential targets for phylogenetic analysis or molecular detection.

Aims: To explore a prokaryotic species-specific DNA marker, 16S-23S rRNA gene internal transcribed spacer (ITS) sequence for identification and classification of Vibrio. Methods and Results: Five hundred and seventy four ITS sequences from 60 Vibrio strains were collected, then the primary and secondary structures of ITS sequence were analysed. The ITS was divided into several subunits, and the species-specificity of these subunits were evaluated by BLAST. The variable subunit of ITS showed high species-specificity. A protocol to identify a Vibrio species based on ITS analysis was developed and verified. Both the specificity and sensitivity were 100%. The phylogeny analysis of Vibrio based on ITS showed that ITS devised a better classification than 16S rDNA. Finally, an identification method of Vibrio based on ITS sequencing in food samples was developed and evaluated. The results of ITS sequencing were (100%) consistent with the results identified by ISO standard. Conclusions: Vibrio could be accurately identified at the species level by using the ITS sequences. Significance and Impact of the Study: The present study suggests that the ITS can be considered as a significant DNA marker for identification and classification of Vibrio species, and it posed a new path to screen the Vibrio in food sample.

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It is a very important significance to explore the bacterial typing methods rapidly, accurately and understand the genetic relation between isolates for controlling effectively the disease and preventing the dissemination and diffusion of the pathogen. The changes in the genetic material nucleotide sequences result in variation and evolution of bacteria, the development of molecular biology and genomics make typing of bacteria from phenotype to molecular typing. Riemerella anatipestifer is the causative agent of polyserositis of ducks and geese. We studied 54 isolates of Riemerella anatipestifer from Guangdong in China by multicolor sequence typing (MLST). The result showed that 54 isolates of Riemerella anatipestifer were divided into 14 STs, and among E3, b12xiao and Cb1 three isolates have with independent of type STs. It was found that there was high homology of RA and low genetic variability in the same area. The synonymous mutation and non synonymous mutation rate: dN/dS in seven housekeeping genes was lower than 0.25. Cluster analysis showed that the 54 isolates were clustered into 5 groups. eBRUST analysis showed that all isolates were clustered into one Group. It also proved that the genetic relationship was very closed in duck plague pathogen in this area; the source may be the same ancestors.