TABLE 3.
Summary of group-specific qPCR primers
| Target group | Sequence | Annealing temp (°C) | Amplicon size (bp) | Reference strain | Reference |
|---|---|---|---|---|---|
| Universal | GTGSTGCAYGGYYGTCGTCA | 60 | 141 | Ruminococcus bromii L2-63 | 35 |
| ACGTCRTCCMCNCCTTCCTC | |||||
| Prevotella spp. | CRCRCRGTAAACGATGGATG | 65 | 105 | Prevotella copri DSM18205 | 33 |
| TTGAGTTTCACCGTTGCCGG | |||||
| Bacteroides spp. | GCTCAACCKTAAAATTGCAGTTG | 63 | 110 | Bacteroides thetaiotaomicron B5482 | 33 |
| GCAATCGGRGTTCTTCGTG | |||||
| Lactobacillus spp. | AGCAGTAGGGAATCTTCCA | 60 | 341 | Lactobacillus reuteri DSM20016 | 36 |
| CACCGCTACACATGGAG | 37 | ||||
| Bifidobacteria | TCGCGTCYGGTGTGAAAG | 60 | 128 | Bifidobacterium adolescentis DSM20083 | 35 |
| GGTGTTCTTCCCGATATCTACA | |||||
| Enterobacteria | GACCTCGCGAGAGCA | 60 | 180 | Escherichia coli XL1-Blue | 38 |
| CCTACTTCTTTTGCAACCCA | |||||
| Cluster IV Ruminococcaceae family | GCACAAGCAGTGGAGTa | 60 | 241 | R. bromii L2-63 | 39 |
| GCACAAGCGGTGGATTa | |||||
| CTTCCTCCGTTTTGTCAA | |||||
| Cluster IX Negativicutes class | GTTGTCCGGAATYATTGGGC | 63 | 321 | Megasphaera elsdenii LC1 | 40 |
| ATTGCGTTAACTCCGGCACAb | |||||
| ATTGCGTTAACTCCGGCACGb | |||||
| Cluster XIVa Lachnospiraceae family | CGGTACCTGACTAAGAAGC | 60 | 429 | Roseburia hominis A2-183 | 34 |
| AGTTTYATTCTTGCGAACG |
a
Both forward primers for cluster IV were used together at an equimolar concentration.
b
Both reverse primers for cluster IX primers were used together at an equimolar concentration.