Bacterial group | Primer | Reference | q-PCR conditions |
Total bacteria | F-Eub 338 (ACTCCTACGGGAGGCAGCAG) R-Eub 518 (ATTACCGCGGCTGCTGG) | [26] | Initial denaturation: 1 cycle at 50˚C for 2 min and 95˚C for 10 min. Primer annealing and product elongation: 40 cycles at 95˚C for 15 s and 60˚C for 1 min. |
Lactobacilli | F-lacto (GAGGCAGCAGTAGGGAATCTTC) R-lacto (GGCCAGTTACTACCTCTATCCTTCTTC) | [27] | Idem |
Enterobacteria | F5 (ATGGCTGTCGTCAGCTCGT) R5 (CCTACTTCTTTTGCAACCCACTC) | [28] | Idem |
Bacteroides | AllBac296F (GAGAGGAAGGTCCCCCAC) AllBac412R (CGCTACTTGGCTGGTTCAG) | [29] | Idem |
C. coccoides/ E. rectale group | g-Ccoc-F (AAATGACGGTACCTGACTAA) g-Ccoc-R (CTTTGAGTTTCATTCTTGCGAA) | [30] | Initial denaturation: 94˚C for 5 min. Primer annealing and product elongation: 40 cycles at 94˚C for 20 s, 50˚C for 20 s, and 72˚C for 1 min. |
C. leptum | sg-Clept-F (GCACAAGCAGTGGAGT) sg-Clept-R3 (CTTCCTCCGTTTTGTCAA) | [30] | Idem |
Escherichia/ Shigella group | F5 (GTTAATACCTTTGCTCATTGA) R5 (ACCAGGGTATCTAATCCTGTT) | [31] | Initial denaturation: 95˚C for 10 min. Primer annealing and product elongation: 35 cycles at 95˚C for15 s, 60˚C for 20 s, and 72˚C for 30 s. |