TABLE 4.

Phylogenetic affiliations of 17 EUB353-negative clones and 9 EUB353-positive clones selected from 16S rDNA clone libraries generated by competitive clamping (clone libraries B1 to B3) and standard PCR of total community rDNA, respectively

Phylogenetic groupa	Clone	Closest phylogenetic neighbor in databaseb	% Sequence similarityc	Accession no.
Cluster related to GNS bacteria	B1-7	rDNA clone SJA-116	99.7	AJ009487
	B1-10	rDNA clone SJA-170	86.2	AJ009500
	B1-12	rDNA clone SJA-170	88.4	AJ009500
	B1-13	rDNA clone SJA-131	99.4	AJ009492
	B1-14	rDNA clone SJA-170	85.9	AJ009500
	B1-15	rDNA clone WCHB1-50	95.6	AF050566
	B1-16	rDNA clone SJA-116	99.4	AJ009487
	B1-18	rDNA clone SJA-61	99.4	AJ009469
	B2-3	rDNA clone SJA-108	100	AJ009483
	B2-8	rDNA clone SJA-170	88.7	AJ009500
	B2-10	rDNA clone SJA-61	99.7	AJ009469
	B3-4	rDNA clone SJA-116	99.7	AJ009487
	B3-8	rDNA clone SJA-58	99.4	AJ009468
NKB19	B1-9	rDNA clone NKB19	84.1	AB013271
	B1-11	rDNA clone NKB19	83.8	AB013271
	B3-6	rDNA clone NKB19	84.1	AB013271
Low-G+C-content gram-positive bacteria	B3-14	rDNA clone SJA-19	99.4	AJ009454
α-Proteobacteria	B4-53	rDNA clone SBR1100	96.0	X84528
	B4-62	rDNA clone SJA-53	98.0	AJ009467
β-Proteobacteria	B4-68	rDNA clone SJA-186	99.7	AJ009507
	B5-11	rDNA clone SJA-186	99.7	AJ009507
	B6-52	rDNA clone SJA-186	99.4	AJ009507
	B6-60	rDNA clone SJA-186	99.4	AJ009507
γ-Proteobacteria	B4-69	Pseudomonas sp. strain RNA-111	100	AJ387903
δ-Proteobacteria	B5-4	rDNA clone SJA-51	96.9	AJ009465
Low-G+C-content gram-positive bacteria	B6-59	Clostridium quercicolum	90.2	M59110

^aα-, β-, γ-, and δ-Proteobacteria, α, β, γ, and δ subdivisions of the Proteobacteria, respectively. 

^bReferences were as follows: SJA rDNA clones, reference 23; rDNA clone WCHB1-50, reference 6; rDNA clone NKB19, reference 14; rDNA clone SBR100, reference 4; and strain RNA-111, reference 24. 

^cBased on comparisons with E. coli positions 7 to 347.