TABLE 1.

PCR primers and probe used in this study

Primer	Sequence (5′→3′)	Annealing positiona	Target	Annealing temp (°C)	Amplicon length (bp)b	Reference
27f	AGA GTT TGA TCM TGG CTC AG	8–27	Most bacteria	54	1,535	38
1525r	AAG GAG GTG WTC CAR CC	1,525–1,542
340f	TCC TAC GGG AGG CAG CAG T	340–258	Most bacteria	60	467	76
806r	GGA CTA CCA GGG TAT CTA ATC CTG TT	781–806
TaqMan probe	6-FAM-5′-CGT ATT ACC GCG GCT GCT GGC AC-3′-TAMRA	515–537
Bac303f	GAA GGT CCC CCA CAT TG	302–318	Bacteroides	56	418	41
Bac708r	CAA TCG GAG TTC TTC GTG	708–725				77
Bif164f	GGG TGG TAA TGC CGG ATG	164–181	Bifidobacterium	60	530	78
Bif662rc	CCA CCG TTA CAC CGG GAA	676–693
ECA75f	GGA AGA AGC TTG CTT CTT TGCT GAC	75–99	E. coli	56	545	44
ECR619r	AGC CCG GGG ATT TCA CAT CTG ACT TA	594–619
Cdif-706f	ATT AGG AGG AAC ACC AGT TG	164–181	C. difficile	54	307	43
Cdif-994r	AGG AGA TGT CAT TGG GAT GT	994–1,012
BiLON-1	TTC CAG TTG ATC GCA TGG TC	186–207	B. longum	63	831	42
BiLON-2	GGG AAG CCG TAT CTC TAC GA	1,009–1,028
ERIC 1	ATG TAA GCT CCT GGG GAT TCA C	Variable	Bacteria	52	Variable	37
ERIC 2	AAG TAA GTG ACT GGG GTG AGC G

^aBased on numbering of the rrs gene of Bacteroides.

^bCalculated based on the rrs gene of Bacteroides.

^cWhen used in PCR-DGGE, a 40-bp GC clamp (5′-CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG G-3′) was attached to the primer at the 5′ end.