Table 2. Probes used for fluorescent in-situ hybridisation (FISH).
| Probe | 16S rDNA position a b | Probe sequence c | Fluorophore | Reference |
| Universal | ||||
| Eub A | 338–355 a | 5′ - GCT GCC TCC CGT AGG AGT - 3′ | Rhodamine red | [20] |
| Eub B | 338–355 a | 5′ - GCT GCC ACC CGT AGG TGT - 3′ | Rhodamine red | [40] |
| Eub C | 338–355 a | 5′ - GCA GCC ACC CGT AGG TGT - 3′ | Rhodamine red | [40] |
| Helicobacteraceae family specific | ||||
| Hgen1 | 218–235 b | 5′- ARC TGA TAG GAC ATA GRC - 3′ c | Cy3 | This study |
| Hgen2 | 666–683 b | 5′ - TGA GTA TTC YTC TTG ATM - 3′ c | Oregon green 488 | This study |
| Hgen3 | 657–674 b | 5′ - CTC TTG ATC TCT ACG GAT - 3′ | Oregon green 488 | This study |
| Hgen4 | 630–647 b | 5′ - ACA CCA AGA ATT CCA CCT - 3′ | Oregon green 488 | This study |
| Hgen5 | 1047–1067 b | 5′ - GCC GTG CAG CAC CTG TTT TCA - 3′ | Oregon green 488 | This study |
| Helicobacter pylori specific | ||||
| Hpy-1 | 547–567 b | 5′- CACACCTGACTGACTATCCCG - 3′ | Cy3 | [21] |
| HP2 | 796–815 b | 5′- CTG GAG AGA CTA AGC CCT CC - 3′ | Oregon green 488 | [16] |
| Hp16S-1 | 163–185 b | 5′- GGAGTATCTGGTATTAATCATCG - 3′ | Oregon green 488 | [41] |
| Hp16S-2 | 206–227 b | 5′- GGACATAGGCTGATCTCTTAGC -3′ | Oregon green 488 | [41] |
a
Indicates E. coli numbering.
b
Indicates H. pylori numbering to strain 26695 (ATCC 700392).
c
Indicates degeneracy of nucleotides according to IUPAC see http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html.