Phylogenetic Analysis of Salmonella , Shigella , and Escherichia coli Strains on the Basis of the gyrB Gene Sequence

Abstract

Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species.

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

“…These results and further inspection of leader sequences indicate that the 14 strains listed above employ an essentially identical attenuation control mechanism for pyrimidine-mediated regulation of pyrBI expression. The results are also consistent with the established evolutionary relationships among strains of Escherichia, Shigella, and Salmonella (41).…”

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

“…The 16S rRNA gene sequence similarity value of 99.5 % between species within a genus is higher than the reported range of 98.2-99.0 % (Kim et al, 2014;Meier-Kolthoff et al, 2013;Stackebrandt & Ebers, 2006;Yarza et al, 2008). However, there are genera such as Brucella, Burkholderia, Bacillus, Brevundimonas, Escherichia, Salmonella and Shigella that contain separate species that share 100 % 16S rRNA gene sequence similarity (Ash et al, 1991;Fukushima et al, 2002;Gee et al, 2004;Gevers et al, 2005;Jaspers & Overmann, 2004). Tables 1-3 summarize physiological and genomic properties that can be used to differentiate strains ACB1 T , ACB7 T and ACB8 from O. sinus and other members of the genus.…”

Detection and Identification of Mycobacterium Species Isolates by DNA Microarray

“…They used these gyrB genes in the taxonomic classification of Pseudomonas putida and Acinetobacter strains. We have reported that such closely related bacteria, for example, Shigella and Escherichia coli, might be classified by gyrB analysis (12). The rate of molecular evolution inferred from gyrB gene sequences is faster than that inferred from 16S rRNA gene sequences.…”