Table 1. Universal and group-specific 16S rRNA gene-targeted primers and PCR/DGGE conditions.

Primer	Sequence (5′→3′)	Amplicon size (bp)	PCR	DGGE			Target group	Reference
			Annealing temp (°C)	Acrylamide (%)	Gradient (%)	Run
341F	CCTACGGGAGGCAGCAGCCG*	585	56	6	36–54	90 V/16 h	Universal bacteria (16S rRNA gene variable regions V3–V5)	Muyzer & Smalla (1998)
907R	TCAATTCMTTTGAGTTT
BfraF	GGTGTCGGCTTAAGTGCCAT	140	62	8	40–65	135 V/5 h	Bacteroides–Prevotella–Porphyromonas	Rinttilä et al. (2004)
BfraR	CGGA(C/T)GTAAGGGCCGTGC*
BifF	GCGTGCTTAACACATGCAAGTC	125	60	8	40–70	135 V/5 h	Bifidobacteria	Zwielehner et al. (2009)
BifR	CACCCGTTTCCAGGAGCTATT*
CoccoF	AAATGACGGTACCTGACTAA	440	53	6	38–58	70 V/16 h	Clostridium coccoides	Matsuki et al. (2002)
CoccoR	CTTTGAGTTTCATTCTTGCGAA*
LacF	AGCAGTAGGGAATCTTCCA	380	56	8	38–53	70 V/16 h	Lactobacilli	Vanhoutte et al. (2004)
LacR	ATTYCACCGCTACACATG*

F, Forward; R, reverse.

^*GC clamp, CGCCCGGGGCGCGCCCCGGGCGGGGCGGGGGCACGGGGGG.