[Comparison between relative analogy and homology of 16S rRNA partial sequences between Mycobacterium szulgai and Mycobacterium malmoense].
A lot of nucleotide sequences of some genes, especially 16S rRNA gene, are registered in the public data-base. In order to identify clinical mycobacterial strains, 16S rRNA gene partial nucleotide sequences from 15 strains of Mycobacterium malmoense and 24 strains of Mycobacterium szulgai which are stored in the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association were determined. Then homology of the sequences to the data of type strains submitted to public database were determined. Relative analogy to type strains by delta DDH was also measured. In the area of nucleotide position 51-588 corresponding accession number X52930 which is Mycobacterium malmoense type strain 16S rRNA gene sequence data, the homology of some partial sequences with Mycobacterium malmoense strains to data of accession number X52930 were lower than that with Mycobacterium szulgai type strain data, accession number X52926. In the area of nucleotide position 31-568 or nucleotide position 31-588, the homology of all nucleotide sequence data to collect species data of type strains were higher than the homology to another species data. Nucleotide position 38, 40, 47 and 49 might be differential nucleotides conserved between Mycobacterium malmoense strains and Mycobacterium szulgai one. These results suggest that homology of about 500 bp's 16S rRNA gene nucleotide sequence data may not be enough for differential identification. Nevertheless, database of RIDOM, Ribosomal differentiation of Medical Microorganisms, identified partial nucleotide sequences between nucleotide position 51-588 corresponding accession number X52930 correctly, though some were lower than 97% homology (data not shown). Therefore quality-controlled 16S rRNA gene nucleotide sequence database could be used for differential identification.
Fukasawa
Yutaka
Y
Department of Microbiology and Bioinformatics, Gifu University Graduate School of Medicine, 40 Tsukasa-machi, Gifu-shi, Gifu 500-8705, Japan. h2801105@guedu.cc.gifu-u.ac.jp
D004269:DNA, Bacterial / Q000032:analysis; D009170:Nontuberculous Mycobacteria / Q000145:classification / Q000235:genetics*; D009693:Nucleic Acid Hybridization / Q000379:methods; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S