Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains

Abstract

Twenty-one strains of Saccharomonospora azurea, Saccharomonospora cyanea, Saccharomonospora glauca, Saccharomonospora viridis, and 'Saccharomonospora caesia' were examined to evaluate the discriminatory value of 16S ribosomal DNA (rDNA) fingerprints. The 16S rDNAs were amplified by PCR by using oligonucleotide primers complementary to 16S rRNA genes. A restriction fragment length polymorphism (RFLP) analysis of the 16S rDNAs was performed with Smal and MluI. The four validly described Saccharomonospora species could be differentiated on the basis of their characteristic 16S rDNA restriction patterns. The strains of 'S. caesia' gave a restriction pattern identical to that of S. azurea K161(T) (T = type strain). This result was anticipated from the previous report that S. azurea K161(T) and the strains of 'S. caesia' have identical 16S rRNA sequences. We found that purification of amplified 16S rDNA products following PCR was necessary for our RFLP analysis.