Table 1.
Primers targeting 16S rRNA gene used for determination of luminal- and mucosa-associated microbiota composition by real time PCR.
| Target group or organism | Sequence (5′ to 3′) | Annealing temperature, °C | Reference |
|---|---|---|---|
| All bacteria (domain bacteria) |
F: ACTCCTACGGGAGGCAGCAG R: ATTACCGCGGCTGCTGG |
60 | Clifford et al., 2012 |
| Bacteroides spp. | F: GAGAGGAAGGTCCCCCAC R: CGCTACTTGGCTGGTTCAG |
58 | Peinado et al., 2013 |
| Lactobacillus spp. | F: GAGGCAGCAGTAGGGAATCTTC R:GGCCAGTTACTACCTCTATCCTTCTTC |
60 |
Delroisse et al., 2008; Peinado et al., 2013 |
| Bifidobacterium spp. | F: CGCGTCYGGTGTGAAAG R: CCCCACATCCAGCATCCA |
58 |
Delroisse et al., 2008; Peinado et al., 2013 |
| Escherichia coli | F: CATGCCGCGTGTATGAAGAA R:GGGTAACGTCAATGAGCAAAGG |
60 | Silkie and Nelson, 2009 |
|
Clostridium perfringens subgroup (Clostridium cluster I) |
F: TACCHRAGGAGGAAGCCAC R:GTTCTTCCTAATCTCTACGCAT |
56 | Goodarzi Boroojeni et al., 2014 |
|
Clostridium leptum subgroup (Clostridium cluster IV) |
F: GCACAAGCAGTGGAGT R: CTTCCTCCGTTTTGTCAA |
52 | Matsuki et al., 2004 |
|
Clostridium coccoides subgroup (Clostridium cluster XIVa) |
F: ACTCCTACGGGAGGCAGC R:CTTCTTAGTCAGGTACCGTCAT |
60 | Schwiertz et al., 2010 |