Phylogenetic Analysis of 16S rDNA of Eubacterium exiguum and the Species-specific Regions for Primer Designation.
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<I>Eubacterium exiguum</I> 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. <I>exiguum</I> (the type strain ATCC 700122 and 3 clinical strains) and compared with those of related oral AAGPR, including <I>Cryptobacterium curtum, E. brachy, E. minutum, E. nodatum, E. saphenum, Mogibacterium timidum</I> (former E. <I>timidum</I>). The 16S rDNA sequence of E. <I>exgiuum</I> 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. <I>exiguum</I> 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), of 13 primers prepared according to the species-specific regions, were effective for PCR amplification of 16S rDNA taken from E. <I>exiguum</I> strains, ATCC 700122, IT-b, TU-d and ABg-f, respectively. Among these, only one combination (exg 557F+exg 1263R) was found to be species-specific, because only that combination did not show any non-specific amplification with any DNA obtained from various oral bacterial strains, and the primer pair can be used to detect E. <I>exiguu</I> in various clinical samples.
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