TABLE 1.
16S rRNA gene-targeted group-specific primers used in this study
| Target group | Primera | Sequence (5′–3′)b | Amplicon length (bp) | Source or reference |
|---|---|---|---|---|
| Bacteroidetes | Bac960F | GTTTAATTCGATGATACGCGAG | 122 | This study |
| Bac1100R | TTAASCCGACACCTCACGG | 122 | This study | |
| Firmicutes | Firm934F | GGAGYATGTGGTTTAATTCGAAGCA | 126 | 9 |
| Firm1060R | AGCTGACGACAACCATGCAC | 126 | 9 | |
| Actinobacteria | Act664F | TGTAGCGGTGGAATGCGC | 277 | This study |
| Act941R | AATTAAGCCACATGCTCCGCT | 277 | This study | |
| “Candidatus Saccharibacteria” | Sac1031F | AAGAGAACTGTGCCTTCGG | 187 | This study |
| Sac1218R | GCGTAAGGGAAATACTGACC | 187 | This study | |
| Deferribacteres | Defer1115F | CTATTTCCAGTTGCTAACGG | 150 | This study |
| Defer1265R | GAGHTGCTTCCCTCTGATTATG | 150 | This study | |
| Verrucomicrobia | Ver1165F | TCAKGTCAGTATGGCCCTTAT | 97 | This study |
| Ver1263R | CAGTTTTYAGGATTTCCTCCGCC | 97 | This study | |
| Tenericutes | Ten662F | ATGTGTAGCGGTAAAATGCGTAA | 200 | This study |
| Ten862R | CMTACTTGCGTACGTACTACT | 200 | This study | |
| Betaproteobacteria | Beta979F | AACGCGAAAAACCTTACCTACC | 174 | This study |
| Beta1130R | TGCCCTTTCGTAGCAACTAGTG | 174 | This study | |
| Epsilonproteobacteria | Epsilon940F | TAGGCTTGACATTGATAGAATC | 189 | This study |
| Epsilon1129R | CTTACGAAGGCAGTCTCCTTA | 189 | This study | |
| Delta- and Gammaproteobacteria | Gamma877F | GCTAACGCATTAAGTRYCCCG | 189 | This study |
| Gamma1066R | GCCATGCRGCACCTGTCT | 189 | This study | |
| Universal | 926F | AAACTCAAAKGAATTGACGG | 136 | 12 |
| 1062R | CTCACRRCACGAGCTGAC | 136 | 12 | |
| Bacterial 16S rRNA | 27F | AGAGTTTGATCCTGGCTCAG | 18 | |
| 1525R | AAGGAGGTGWTCCARCC | 18 |
a
Numbers within the primer name indicate the nucleotide position based on the Escherichia coli ATCC 11775T 16S rRNA gene.
b
Nucleotide symbols: R = A or G; Y = C or T; N = any nucleotide; W = A or T; M = A or C; K = T or G; S = C or G; and H = A/C/T.