Main target |  | rRNA gene | Sequence (5′ → 3′) | E. coli position | Size, bp | Reference | Reference bacterium |
---|---|---|---|---|---|---|---|
Domain Bacteria A V2-V3 | Forward | 16S | AGAGTTTGATCCTGGCTCAG | 7 | 336 | Liu et al.[30] | 1,2,3,4,5,6,7,8,9,10,11,13,14,15 |
Reverse | 16S | CTGCTGCCTYCCGTA | 342 | Liu et al.[30] | |||
Domain Bacteria B V4-V5 | Forward | 16S | CAGCAGCCGCGGTAATAC | 518 | 389 | Schwieger & Tebbe [31] | 1,2,3,4,5,6,7,8,9,10,11,13,14,15 |
Reverse | 16S | CCGTCAATTCCTTTGAGTTT | 906 | Schwieger & Tebbe [31] | |||
Phylum Firmicutes | Forward | 16S | CTGATGGAGCAACGCCGCGT | 385 | 429 | Haakensen et al.[32] | 6,7,9,11,13,14 |
Reverse | 16S | ACACYTAGYACTCATCGTTT | 813 | Mühling et al.[33] | |||
Class Bacilli | Forward | 16S | GCAGTAGGGAATCTTCCGC | 353 | 461 | Felske et al.[34] | 7,11,14 |
Reverse | 16S | ACACTTAGCACTCATCGTTT | 813 | Modified from Mühling et al.[33] | |||
Genus Enterococcus | Forward | 16S | GGGTAACCTRCCCATCAGA | 125 | 325 | Modified from Behr et al.[35] | 7 |
Reverse* | 16S 16S | GTTACTCTCATCCTTGTTC ACCGTCAGGGGACGTTCAG | 449 466 | 342 | Modified from Behr et al.[35] Modified from Behr et al.[35] | ||
Genus Lactobacillus | Forward | 23S | GCGGTGAAATTCCAAACG | 774 | 216 | This study, Linux ARB [13] | 11 |
Reverse | 23S | GGGACCTTAACTGGTGAT | 989 | This study, Linux ARB [13] | |||
Genus Streptococcus | Forward | 16S | CTWACCAGAAAGGGACGGCT | 488 | 337 | This study, ClustalW2 [36] | 14 |
Reverse | 16S | AAGGRYCYAACACCTAGC | 824 | This study, ClustalW2 [36] | |||
Family Clostridium cluster I | Forward | 16S | AAAGGAAGATTAATACCGCATA | 159 | 538 | Modified from Rinttila et al.[37] | 6 |
Reverse | 16S | TTCTTCCTAATCTCTACGCA | 696 | Hung et al.[38] | |||
Species Clostridium perfringens | Forward | 16S | TGAAAGATGGCATCATCATTCAAC | 183 | 258 | Skånseng et al.[39] | 6 |
Reverse | 16S | GGTACCGTCATTATCTTCCCCAAA | 440 | Skånseng et al.[39] | |||
Family Clostridium cluster IV | Forward | 16S | ACAATAAGTAATCCACCTGG | 866 | 298 | Modified from Ramirez-Farias et al.[40] | 9 |
Reverse | 16S | CTTCCTCCGTTTTGTCAA | 1163 | Matsuki et al.[41] | |||
Family Clostridium cluster XIV | Forward | 16S | CGGTACCTGACTAAGAAGC | 482 | 413 | Rinttila et al.[37] | 13 |
Reverse | 16S | CTTTGAGTTTCATTCTTGCGAA | 894 | Matsuki et al.[42] | |||
Phylum Bacteroidetes | Forward | 16S | CCGGAWTYATTGGGTTTAAAGGG | 554 | 414 | Mühling et al.[33] | 1 |
Reverse | 16S | GGTAAGGTTCCTCGCGTA | 967 | Mühling et al.[33] | |||
Genus Bacteroides | Forward | 16S | AAGGTCCCCCACATTGG | 302 | 300 | Manz et al.[43] | 1 |
Reverse | 16S | GAGCCGCAAACTTTCACAA | 601 | Franks et al.[44] | |||
Phylum Actinobacteria | Forward | 16S | GCGKCCTATCAGCTTGTT | 235 | 333 | Modified from Glockner et al.[45] first published. They refer to Erhart [46] | 2 |
Reverse | 16S | CCGCCTACGAGCYCTTTACGC | 567 | This study, ClustalW2 [36] | |||
Family Bifidobacteriaceae | Forward | 16S | CTCCTGGAAACGGGTGG | 152 | 442 | Matsuki et al.[42] | 2 |
Reverse | 16S | CTTTCACACCRGACGCG | 593 | Delroisse et al.[47] | |||
Class β- and γ-proteobacteria | Forward | 23S | GTATAATGGGTCAGCGAC | 569 | 673 | This study, Linux ARB [13] | 8 |
Reverse | 23S | CAGCATTCGCACTTCTGA | 1241 | This study, Linux ARB [13] | |||
Family Enterobacteriacea | Forward | 16S | CGTCGCAAGMMCAAAGAG | 182 | 333 | Modified from Friedrich et al.[48] | 8 |
Reverse | 16S | TTACCGCGGCTGCTGGCAC | 514 | Modified from Palmer et al.[49] | |||
Species Escherichia coli | Forward | 16S | GTTAATACCTTTGCTCATTGA | 461 | 320 | Malinen et al.[50] | 8 |
Reverse | 16S | ACCAGGGTATCTAATCCTGTT | 780 | Malinen et al.[50] | |||
Class ϵ-proteobacteria | Forward | 16S | TGGTGTAGGGGTAAAATCCG | 680 | 286 | Bui et al.[51] | 5 |
Reverse | 16S | AGGTAAGGTTCTTCGYGTATC | 965 | This study, Primrose [14] | |||
Class δ-proteobacteria | Forward | 16S | GGTGTAGGAGTGAARTCCGT | 681 | 534 | This study, Primrose [14] | 3 |
Reverse | 16S | TACGTGTGTAGCCCTRGRC | 1214 | This study, Primrose [14] | |||
Phylum Fusobacteria | Forward | 16S | GATCCAGCAATTCTGTGTGC | 387 | 292 | Sanguin et al.[52] | 10 |
Reverse | 16S | CGAATTTCACCTCTACACTTGT | 678 | Walter et al.[53] | |||
Phylum Verrucomicrobia | Forward | 16S | GAATTCTCGGTGTAGCA | 673 | 551 | Modified from Ranjan [54] | 15 |
Reverse | 16S | GGCATTGTAGTACGTGTGCA | 1223 | This study, Primrose [14] | |||
Phylum Spirochaetes | Forward | 16S | GTYTTAAGCATGCAAGTC | 45 | 294 | Choi et al.[55] | 4 |
Reverse | 16S | TGCTGCCTCCCGTAGGAG | 338 | This study, ClustalW2 [36] | |||
Domain Archaea | Forward | 16S | CAGCMGCCGCGGTAATWC | 518 | 440 | Giovannoni et al.[56] | 12 |
Reverse | 16S | YCCGGCGTTGAMTCCAATT | 957 | Delong [57] |