Species-identification dots: a potent tool for developing genome microbiology.
Identification of species has long been done by phenotype-based methodologies. Recently, genotype-based species identification has been shown to be possible by way of Genome profiling, which is based on a temperature gradient gel electrophoresis (TGGE) analysis of random PCR products. However, the results, though sufficient in information, provided by genome profiling were complicated and difficult to deal with objectively. To cope with this, a technology of utilizing species identification dots (spiddos), which corresponds to structural transition points of DNAs, was introduced. Pattern similarity score (PaSS), derived from spiddos, was shown to be usable for quantitatively measuring the closeness between genomes. This was demonstrated with the experiments applied to the genomes of Escherichia coli O157:H7 (19 strains). The same genomes were also examined by sequencing and RFLP methods in order to compare the effectiveness of these three methods. As a result, the spiddos method was shown to give reasonable results and to be the most advantageous for measuring the closeness between species in general. This means that spiddos is pushing the heavy gate open for genome microbiology.
Naimuddin
M
M
Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Urawa, 338-8570, Saitama, Japan.
Kurazono
T
T
Zhang
Y
Y
Watanabe
T
T
Yamaguchi
M
M
Nishigaki
K
K
D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D004591:Electrophoresis, Polyacrylamide Gel; D019453:Escherichia coli O157 / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial; D005838:Genotype; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013045:Species Specificity
D004269:DNA, Bacterial