Application of Sequence-Dependent Electrophoresis Fingerprinting in Exploring Biodiversity and Population Dynamics of Human Intestinal Microbiota: What Can Be Revealed?

Table 2

Universal and group-specific PCR primers used in SDE-based profiling of human intestinal microbial communities.

Target group(s)	Primer designation	Sequence (5^′-3^′)^a	Target region	Selected reference(s)
Domain level
Bacteria	HDA1^b	ACTCCTACGGGAGGCAGCAGT	V2-V3-16S rDNA	[30, 76, 102, 110–114]
	HDA2^b	GTATTACCGCGGCTGCTGGCAC
	F357	CCTACGGGAGGCAGCAG	V3-16S rDNA	[64, 72, 73, 77, 79, 115–117]
	518R	ATTACCGCGGCTGCTGG
	339F^c	CTCCTACGGGAGGCAGCAG	V3-V4-16S rDNA	[94, 106, 107]
	788R	GGACTACCAGGGTATCTAA
	U968-F	AACGCGAAGAACCTTAC	V6–V8-16S rDNA	[6, 64, 65, 69, 71, 79, 80, 82, 84, 85, 91, 95, 96, 101, 105, 109, 117–123]
	L1401-R	CGGTGTGTACAAGACCC
Genus (group) level
Bacteroides	FD1	AGAGTTTGATCCTGGCTCAG	16S rDNA	[124]
	RbacPre	TCACCGTTGCCGGCGTACTC
	Bfr-F	CTGAACCAGCCAAGTAGCG	16S rDNA	[81]
	Bfr-R	CCGCAAACTTTCACAACTGACTTA
Bifidobacterium	Bif164-f	GGGTGGTAATGCCGGATG	16S rDNA	[69, 79, 82, 85, 99, 101, 105, 108, 118, 125–127]
	Bif662-r	CCACCGTTACACCGGGAA
	g-Bifid-F	CTCCTGGAAACGGGTGG	16S rDNA	[64]
	g-Bifid-R	GGTGTTCTTCCCGATATCTACA
	ForTal	CGTCGCCTTCTTCTTCGTCTC	transaldolase gene	[74]
	RevTal	CTTCTCCGGCATGGTGTTGAC
Helicobacter	658f	TGGGAGAGGTAGGTGGAAT	16S rDNA	[128]
	1067R	GCCGTGCAGCACCTGTTTTCA
Enterococcus	Ent1017F	CCTTTGACCACTCTAGAG	16S rDNA	[64]
	Ent1263R	CTTAGCCTCGCGACT
Lactobacillus group^d	Lac1	AGCAGTAGGGAATCTTCCA	16S rDNA	[64, 86, 88, 125, 127, 129, 130]
	Lac2	ATTYCACCGCTACACATG
	27f (also Bact-0011f)	AGAGTTTGAT(C/T)(A/C)TGGCTCAG	16S rDNA	[79, 98, 118]
	Lab-0677r	CACCGCTACACATGGAG
	Lab-0159f	GGAAACAG(A/G)TGCTAATACCG	16S rDNA	[98, 118]
	Uni-0515-r	ATCGTATTACCGCGGCTGCTGGCA
	Lab-0159f	GGAAACAG(A/G)TGCTAATACCG	16S rDNA	[124]
	Lab-0677r	CACCGCTACACATGGAG
Species group level
Bacteroides fragilis subgroup^e	g-Bact-F	ATAGCCTTTCGAAAGRAAGAT	16S rDNA	[73]
	g-Bact-R	CCAGTATCAACTGCAATTTTA
	Bact 596F	TCAGTTGTGAAAGTTTGCG	16S rDNA	[64]
	Bact 826R	GTRTATCGCMAACAGCGA
	Bact 531F	ATACGGAGGATCCGAGCGTTA	16S rDNA	[90]
	Bact 766R	CTGTTTGATACCCACACT
Clostridium phylogenetic clusters XI and XIVa^f	Erec 688F	GCGTAGATATTAGGAGGAAC	16S rDNA	[90]
	Erec 841R	TGCGTTWGCKRCGGCACCG

^aA GC-clamp is attached to the 5^′ end of either the forward or reverse primer.^bPrimers HDA1 and HDA2 have the same core sequence as primers 341 f and 518 r, respectively, but with a few additional nucleotides at both 5^′ and 3^′ ends.^cPrimer 339f has the same core sequence as primer 341 f but with two additional nucleotides at the 5^′ end.^dThe Lactobacillus group comprising the genera Lactobacillus, Leuconostoc, Pediococcus, Weissella, and Aerococcus (the latter genus was originally not described as target of the Lac1/2 primers).^eThe Bacteroides fragilis subgroup comprising B. fragilis, B. acidifaciens, B. caccae, B. eggerthii, B. ovatus, B. stercoris, B. thetaiotaomicron, B. uniformis, and B. vulgatus.^fClostridium phylogenetic cluster XI represents the Clostridium lituseburense group, whereas Clostridium phylogenetic cluster XIVa represents the Clostridium coccoides-Eubacterium rectale group.