Differentiation of Bifidobacterium species using partial RNA polymerase {beta}-subunit (rpoB) gene sequences.
Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum-Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum-Bifidobacterium pullorum-Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.
Kim
Byoung Jun
BJ
Department of Microbiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
Kim
Hee-Youn
HY
Department of Microbiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
Yun
Yeo-Jun
YJ
Department of Microbiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
Kim
Bum-Joon
BJ
Department of Microbiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
Kook
Yoon-Hoh
YH
Department of Microbiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
D015373:Bacterial Typing Techniques; D001644:Bifidobacterium / Q000145:classification*; D018834:Chaperonin 60 / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
D018834:Chaperonin 60; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit