Table 1.
Primers and probes used in this study
| Name | Sequence (5′ to 3′) | Use | Targeta | Reference |
|---|---|---|---|---|
| 32F | AACGCTAGCTACAGGCTT | PCR and sequencing | Bacteroides genus specific | Bernhard and Field (2000b,b) |
| 708R | CAATCGGAGTTCTTCGTG | PCR | Bacteroides genus specific | Bernhard and Field (2000b,b) |
| 32F‐GCb | CGCCCGGGGCGCGCCCCGGGCGGGGCGGGGGCACGGGGGGAACGCTAGCTACAGGCTT | PCR‐DGGE | Bacteroides genus specific | Myers et al. (1985a,b) |
| 580R | CGCTCCCTTTAAACCCAAT | DGGE‐PCR and sequencing | Bacteroides genus specific | This study |
| pGEMup | tgtaatacgactcactat | PCR and sequencing | pGEM‐T Easy plasmid | Serra‐Moreno et al. (2008) |
| Bac‐FW | GGCGCACGGGTGAGTAAC | qPCR | Uncultured Bacteroides | This study |
| Bac‐Rev | TGTGGGGGACCTTCCTCTC | qPCR | Uncultured Bacteroides | This study |
| HMprobeBac | FAM‐GTGAGGGCATCTAATCA | qPCR probe humans | Uncultured Bacteroides | This study |
| PLprobeBac | FAM‐TCCGCATGAAGGACTT | qPCR probe poultry | Uncultured Bacteroides | This study |
| PGprobeBac | FAM‐TATGATAGCATTAGAGTGTGACGAA | qPCR probe pigs | Uncultured Bacteroides | This study |
| CWprobeBac | FAM‐CTATGGGATGGGGATGC | qPCR probe cattle | Uncultured Bacteroides | This study |
| Bacprobe | FAM‐CGGGGTAACGGCCCA | qPCR common probe | Bacteroides genus specific | This study |
| HF183f | ATCATGAGTTCACATGTCCG | qPCR primers | Human Bacteroides | Seurinck et al. (2005) |
| HF183r | TACCCCGCCTACTATCTAATG | qPCR primers | Human Bacteroides | Seurinck et al. (2005) |
| Pig‐2‐Bac | FAM‐TCCACGGGATAGCC | qPCR probe pigs | Pig Bacteroides | Mieszkin et al. (2009) |
| Pig‐2‐Bac41F | GCATGAATTTAGCTTGCTAAATTTGAT | qPCR primers pigs | Pig Bacteroides | Mieszkin et al. (2009) |
| Pig‐2‐Bac163Rm | ACCTCATACGGTATTAATCCGC | qPCR primers pigs | Pig Bacteroides | Mieszkin et al. (2009) |
| Rum‐2‐Bac | FAM‐ATGAGGTGGATGGAATT | qPCR probe cattle | Cattle Bacteroides | Mieszkin et al. (2010) |
| BacB2‐590F | ACAGCCCGCGATTGATACTGGTAA | qPCR primers cattle | Cattle Bacteroides | Mieszkin et al. (2010) |
| Bac708Rm | CAATCGGAGTTCTTCGTGAT | qPCR primers cattle | Cattle Bacteroides | Mieszkin et al. (2010) |
a
Species that show the highest similarity to the probes according to BLAST analysis (http://blast.ncbi.nlm.nih.gov/Blast.cgi).
b
The GC clamp attached to the 5′ end is denoted in italics.