Table 1.
16S rRNA gene primers used in this study
| Target taxon | Primer | Sequence (5′-3′) | PCR product (bp) | Efficiency (E)b | Reference |
|---|---|---|---|---|---|
| Faecalibacterium prausnitzii | Fprau 07 | CCA TGA ATT GCC TTC AAA ACT GTT | 140 | 1.90 | 64 |
| Fprau 02 | GAG CCT CAG CGT CAG TTG GT | ||||
| Bifidobacterium spp. | F-bifido | CGC GTC YGG TGT GAA AG | 244 | 2.04 | 9 |
| R-bifido | CCC CAC ATC CAG CAT CCA | ||||
| Lactobacillus spp. | Lacto-F | AGC AGT AGG GAA TCT TCC A | 341 | 1.98 | 22, 70 |
| Lacto-R | CAC CGC TAC ACA TGG AG | ||||
| Clostridium leptum subgroup | sg-Clept-F | GCA CAA GCA GTG GAG T | 239 | 2.03 | 38, 63 |
| sg-Clept-R | CTT CCT CCG TTT TGT CAA | ||||
| Clostridium coccoides group | g-Ccoc-F | AAA TGA CGG TAC CTG ACT AA | 440 | 2.02 | 38 |
| g-Ccoc-R | CTT TGA GTT TCA TTC TTG CGA A | ||||
| Firmicutes phylum | Firm934F | GGA GYA TGT GGT TTA ATT CGA AGC A | 126 | 2.01 | 20 |
| Firm1060R | AGC TGA CGA CAA CCA TGC AC | ||||
| Bacteroidetes phylum | Bact934F | GGA RCA TGT GGT TTA ATT CGA TGA T | 126 | 1.98 | 20 |
| Bact1060R | AGC TGA CGA CAA CCA TGC AG | ||||
| Desulfovibrio spp. | DSV691-F | CCG TAG ATA TCT GGA GGA ACA TCA G | 136 | 1.90 | 15 |
| DSV826-R | ACA TCT AGC ATC CAT CGT TTA CAG C | ||||
| V2-V3 16S rRNA regiona | HDA1 | ACT CCT ACG GGA GGC AGC AGT | 200 | 1.98 | 70 |
| HDA2 | GTA TTA CCG CGG CTG CTG GCA C | ||||
| 16S rRNA regiona | TBA-F | CGG CAA CGA GCG CAA CCC | 130 | 2.04 | 10 |
| TBA-R | CCA TTG TAG CAC GTG TGT AGC C |
a
The HDA and TBA primers were used as total bacterial DNA targets to normalize for differences in total DNA concentrations between individual samples.
b
Primer efficiency is calculated from the slope of the standard curve for each primer set, E = 10−1/slope.