TABLE 1.
Primers and probes for PCR, qPCR, RT-qPCR, and FISH used in this study
| Primer or probe | Sequence | Purpose | Source |
|---|---|---|---|
| SFB 16S rRNA (mouse) | F: 5′-AGGAGGAGTCTGCGGCACATTAGC-3 R: 5′-TCCCCACTGCTGCCTCCCGTAG-3′ |
qPCR | (13) |
| SFB 16S rRNA (rat) | GGGTACTTATTGCGTTTGCGACGGCAC | FISH | (4) |
| Eubacteria | F: 5′-ACTCCTACGGGAGGCAGCAGT R: 5′-ATTACCGCGGCTGCTGGC |
Taxon qPCR | (91) |
| Firmicutes | F: 5′-GGAGYATGTGGTTTAATTCGAAGCA R: 5′-AGCTGACGACAACCATGCAC |
Taxon qPCR | (91) |
| Bacteroidetes | F: 5′-GTTTAATTCGATGATACGCG R: 5′-TTAAGCCGACACCTCACG |
Taxon qPCR | (91) |
| Lactobacillus spp. | F: 5′-TGGATGCCTTGGCACTAG R: 5′-AAATCTCCGGATCAAAGCTTAC |
Taxon qPCR | (91) |
| GAPDH | F: 5′-GCACGCCATCACTATCTTCC R: 5′-CATCCACCGTCTTCTGTGTG |
RT-qPCR | (90) |
| β-Defensin 12 | F: 5’- AGACAGCTGTAACCACGACA-3 R: 5’- CTGCAGTTCGGACACCTTCA-3 |
RT-qPCR | (49) |
| β-Defensin 14 | F: 5′-ATGGGCATATTCCTCCTGT-3 R: 5′-CACTTTGCCAGTCCATTGT-3 |
RT-qPCR | (49) |
| Cathelicidin β-1 | F: 5’- CCGTGTCCATAGAGCAGCAG-3 R: 5’- AGTGCTGGTGACGTTCAGATG-3 |
RT-qPCR | (90) |
| IL-10 | F: 5′-CATGCTGCTGGGCCTGAA-3 R: 5′-CGTCTCCTTGATCTGCTTGATG-3 |
RT-qPCR | (81) |
| IFNγ | F: 5′-ACACTGACAAGTCAAAGCCGC-3 R- 5’- AGTCGTTCATCGGGAGCTTG-3 |
RT-qPCR | (81) |
| IL-17F | F: 5’- CTCCGATCCCTTATTCTCCTC-3 R: 5’- AAGCGGTTGTGGTCCTCAT-3 |
RT-qPCR | (89) |
| Mucin-2 | F: 5’- AAACAACGGCCATGTTTCAT-3 R: 5’- GTGTGACACTGGTGTGCTGA-3 |
RT-qPCR | (60) |
| Claudin-1 | F: 5’- GGTGAAGAAGATGCGGATGG-3 R: 5’- TCTGGTGTTAACGGGTGTGA-3 |
RT-qPCR | (60) |
| Occludin-1 | F: 5’- GATGGACAGCATCAACGACC-3 R: 5’- CTTGCTTTGGTAGTCTGGGC-3 |
RT-qPCR | (60) |
| ZO-1 | F: 5’- GCCAACTGATGCTGAACCAA-3 R: 5’- GGGAGAGACAGGACAGGACT-3 |
RT-qPCR | (60) |