Table 1.
Specifications of the 16S rRNA primers used in this study
| Target group (variable region) | Primer designation | Primer sequence (5'-3') | Amplicon size | Annealing temperature | DGGE gradient | Reference |
|---|---|---|---|---|---|---|
| Universal (V3) | F357-GC a 518R |
TACGGGAGGCAGCAG ATTACCGCGGCTGCTGG |
217 | 55°C | 20-70% | Muyzer et al., 1993 |
| Universal (V6-V8) | U968F-GC a L1401-R |
AACGCGAAGAACCTTAC CGGTGTGTACAAGACCC |
489 | 55°C | 20-70% | Zoetendal et al., 1998 |
| Bacteroides fragilis subgroup | Bfra 531F Bfra 766R-GCa |
ATACGGAGGATCCGAGCGTTA CTGTTTGATACCCACACT |
293 | 65°C | 20-70% | Vanhoutte et al., 2006 |
| Bifidobacterium | g-Bifid F g-Bifid R-GCa |
CTCCTGGAAACGGGTGG GGTGTTCTTCCCGATATCTACA |
596 | 65°C | 40-70% | Matsukiu et al., 2002 |
| Lactobacillus groupb | Lac 1 Lac2-GC a |
AGCAGTAGGGAATCTTCCA ATTYCACCGCTACACATG |
380 | 61°C | 35-60% | Walter et al., 2001 |
a Primers with GC clamp at 5' end: CGCCCGCCGCGCCCCGCGCCCGGCCCGCCGCCCCCGCCCC.
b Lactobacillus group comprising the genera Lactobacillus, Leuconostoc, Pediococcus and Weisella.