Table 6.
Primers used in qPCR analysis to determine the microbiota in fecal swabs taken 5 days post-infection with E. coli K88. The efficiency of the qPCR was ≥95% for all primers [22]
| Phylum | Class/Family/Genus | Species /Group | Primer sequence | Amplicon size (bp) |
|---|---|---|---|---|
| Universal | All | All | F - 5′-ACTCCTACGGGAGGCAGCAGT-3′ R - 5′-GTATTACCGCGGCTGCTGGCAC-3’ |
175–199 |
| Firmicutes | All | All | F - 5’-TGAAACTCAAAGGAATTGACG-3′ R - 5′-ACCATGCACCACCTGTC-3’ |
157 |
| Firmicutes | Clostridia | Cluster XIVa | F - 5’-AAATGACGGTACCTGACTAA-3′ R - 5′-CTTTGAGTTTCATTCTTGCGAA-3’ |
438 |
| Firmicutes | Lactobacillus | spp. | F - 5’-AGCAGTAGGGAATCTTCCA-3′ R - 5′-CACCGCTACACATGGAG-3’ |
341 |
| Bacteroidetes | Bacteroides/Prevotella | spp. | F - 5’-GAGAGGAAGGTCCCCCAC-3′ R - 5′-CGCTACTTGGCTGGTTCAG-3’ |
106 |
| Actinobacteria | Bifidobacterium | spp. | F - 5’-CGCGTCYGGTGTGAAAG-3′ R - 5′-CCCCACATCCAGCATCCA-3’ |
244 |
| Proteobacteria | Enterobacter-iaceae | group | F - 5’-CATTGACGTTACCCGCAGAAGAAGC-3′ R - 5′-CTCTACGAGACTCAAGCTTGC-3’ |
195 |