Table 2.
Oligonucleotide probes used in the study for fluorescence in situ hybridisation analysis of bacterial populations
| Probe name and sequence (5′–3′) | Target species | Hybridisation-washing temperature (°C) | References |
|---|---|---|---|
| Bif164 CATCCGGCATTACCACCC | Most Bifidobacterium spp. and Parascardovia denticolens | 50–50 | ( 20 ) |
| Bac303 CCAATGTGGGGGACCTT | Most Bacteroides sensu stricto and Prevotella spp.; all Parabacteroides; Barnesiella viscericola and Odoribacter splanchnicus | 46–48 | ( 21 ) |
| Lab158 GGTATTAGCAYCTGTTTCCA | Most Lactobacillus, Leuconostoc and Weissella spp.; Lactococcus lactis; all Vagococcus, Enterococcus, Melissococcus, Tetragenococcus, Catellicoccus, Pediococcus and Paralactobacillus spp. | 50–50 | ( 22 ) |
| Chris150 TTATGCGGTATTAATCTYCCTTT | Most members of Clostridium cluster I; all members of Clostridium cluster II; Clostridium tyrobutyricum; Adhaeribacter aquaticus and Flexibacter canadensis (family Flexibacteriaceae); (Eubacterium) combesii (family Propionibacteriaceae) | 50–50 | ( 23 ) |
| Erec 482 GCTTCTTAGTCARGTACCG | Most members of Clostridium cluster XIVa; Syntrophococcus sucromutans, (Bacteroides) galacturonicus and (Bacteroides) xylanolyticus, Lachnospira pectinschiza and Clostridium saccharolyticum | 50–50 | ( 23 ) |
| EUB338 I GCTGCCTCCCGTAGGAGT | Total bacteria | 46–48 | ( 24 ) |
| EUB338 II GCAGCCACCCGTAGGTGT | Total bacteria | 46–48 | ( 24 ) |
| EUB338 III GCTGCCACCCGTAGGTGT | Total bacteria | 46–48 | ( 24 ) |
| Rrec584 TCAGACTTGCCGYACCGC | Roseburia – Eubacterium rectale (a component of cluster XIVa) | 50–50 | ( 25 ) |
| Prop853 ATTGCGTTAACTCCGGCAC | Clostridium cluster IX | 50–50 | ( 25 ) |