Phylogenetic Analysis of 16S rDNA of Eubacterium exiguum and the Species-specific Regions for Primer Designation

Abstract

: Eubacterium exiguum is a bacterial species of asaccharolytic anaerobic Gram-Positive rods (AAGPR) that are frequently isolated from human oral lesions. To clarify the phylogenetic relationship among oral AAGPR, we determined 16S rDNA gene sequence of E . exiguum (the type strain ATCC 700122 and 3 clinical strains) and compared with those of related oral AAGPR , including Cryptobacterium curtum, E. brachy, E. minutum, E. nodatum , E. saphenum, Mogibacterium timidum (former E. timidum) . The 16S rDNA sequence of E. exgiuum was high similarity between the type strain ATCC 700122 and 3 clinical strains (>99%) but clearly distinct from those of other oral AAGPR species and some typical oral Gram-Positive bacteria. Certain regions in the 16S rDNA were found to be common among 4 strains of E. exiguum but distinct from other bacterial species, thus the regions were species-specific. In fact, 5 pairs of primers (exg 129F and exg 576R, exg 129F and exg 605R , exg 129F and exg 1263R, exg 557F and exg 1263R, exg 586F and exg 1263R),