TABLE 1.
Real-time quantitative polymerase chain reaction primers used to determine the density of specific microbes and functional microbial genes
| Target group and primer | Sequence (5′-3′) | Annealing temperature | Reference |
| °C | |||
| All bacteria | 60 | (13) | |
| Uni331F | TCCTACGGGAGGCAGCAGT | ||
| Uin797R | GGACTACCAGGGTATCTATCCTGTT | ||
| Butyrate-production gene (BcoA) | 60 | (14) | |
| BcoA-F | GCIGAICATTTCACITGGAAYWSITGGCAYATG | ||
| BcoA-R | CCTGCCTTTGCAATRTCIACRAANGC | ||
| Clostridium cluster IV1 | 50 | (15) | |
| Sg-Clept-F | GCACAAGCAGTGGAGT | ||
| Sg-Clept-R3 | CTTCCTCCGTTTTGTCAA | ||
| Costridium cluster XIVa1 | 50 | (15) | |
| g-Ccoc-F | AAATGACGGTACCTGACTAA | ||
| g-Ccoc-R | CTTTGAGTTTCATTCTTGCGAA | ||
| Bifidobacterium spp. | 60 | (16) | |
| Bif164F | GGGTGGTAATGCCGGATG | ||
| Bif662R | CCACCGTTACACCGGGAA | ||
| Succinivibrio | 60 | (17) | |
| SucDex1F | CGTCAGCTCGTGTCGTGAGA | ||
| SucDex1R | CCCGCTGGCAACAAAGG | ||
| Prevotella spp. | 60 | (17) | |
| PreGen4F | GGTTCTGAGAGGAAGGTCCCC | ||
| PreGen4R | TCCTGCACGCTACTTGGCTG | ||
| Bacteroides fragilis group | 60 | (15) | |
| g-Bfra-F | ATAGCCTTTCGAAAGRAAGAT | ||
| g-Bfra-R | CCAGTATCAACTGCAATTTTA | ||
| Lactobacillus spp. | 60 | (18) | |
| LactoF | TGGAAACAGRTGCTAATACCG | ||
| LactoR | GTCCATTGTGGAAGATTCCC | ||
| Faecalibacterium prausnitzii | 60 | (19) | |
| FpF | CCCTTCAGTGCCGCAGT | ||
| FpR | GTCGCAGGATGTCAAGAC | ||
| Functional gene for hydrogen sulfide | 60 | ||
| DSR1F+ | ACSCACTGGAAGCACGGCGG | (20) | |
| DSR-R | GTGGMRCCGTGCAKRTTHG | (20) | |
| Functional gene for methanogenesis | 60 | ||
| mcrA-F | TTCGGTGGATCDCARAGRGC | (21) | |
| mcrA-R | GBARGTCGWAWCCGTAGAATCC | (21) | |
| Functional gene for secondary bile acids | 60 | ||
| BaiCD-F | CAGCCCRCAGATGTTCTTTG | (unpublished observation)2 | |
| BaiCD-R | GCATGGAATTCWACTGCYTC |
1
Number indicates phylogenetic cluster of Clostridium as defined by Collins et al (22).
2
J Ou, A Heather, J Riddlon, S Curry, and SJD O'Keefe, April 2012.