TABLE 2.
Oligonucleotide probes and their target populations used in this study for FISH analyses
| Probe namea | Target rRNA | Designed target(s) | % FAb | Reference |
|---|---|---|---|---|
| EUB338 (00159) | 16S | Domain Bacteria | 0-50 | 16 |
| EUB338II (00160) | 16S | Phylum Planctomycetes | 0-50 | 16 |
| EUB338III (00161) | 16S | Phylum Verrucomicrobia | 0-50 | 16 |
| NONEUB (00243) | 16S | Control probe complementary to EUB338 | 0-50 | 16 |
| ALF968 (00021) | 16S | Class Alphaproteobacteria, phylum Proteobacteria | 20 | 16 |
| BET42a (00034) | 23S | Class Betaproteobacteria, phylum Proteobacteria | 35 | 16 |
| GAM42a (00174) | 23S | Class Gammaproteobacteria, phylum Proteobacteria | 35 | 16 |
| SRB385 (00300) | 16S | Class Deltaproteobacteria, phylum Proteobacteria | 35 | 16 |
| SRB385Db (00301) | 16S | Class Deltaproteobacteria, phylum Proteobacteria | 35 | 16 |
| HGC69a (00182) | 23S | Phylum Actinobacteria | 25 | 16 |
| GNSB941 (00718) | 16S | Phylum Chloroflexi | 35 | 16 |
| CFX1223 (00719) | 16S | Phylum Chloroflexi | 35 | 16 |
| SPIRO1400 (01004) | 16S | Subgroup of family Spirochaetaceae | 20 | 16 |
| TM7-905 (00600) | 16S | Candidate phylum TM7 | 20 | 16 |
| LGC354A (00195) | 16S | Phylum Firmicutes | 35 | 16 |
| LGC354B (00196) | 16S | Phylum Firmicutes | 35 | 16 |
| LGC354C (00197) | 16S | Phylum Firmicutes | 35 | 16 |
| RUM831 | 16S | Rumen clones in family Ruminococcaceae, phylum Firmicutes | 35 | This study |
| RAL1436 | 16S | Ruminococcus albus-related clones, phylum Firmicutes | 20 | This study |
| RFL155 | 16S | Ruminococcus flavefaciens-related clones, phylum Firmicutes | 45 | This study |
| LAC435 | 16S | Clones in family Lachnospiraceae, phylum Firmicutes | 35 | This study |
| BFI826 | 16S | Butyrivibrio fibrisolvens-related clones, phylum Firmicutes | 35 | This study |
| BAC1080 | 16S | Clones in order Bacteroidales, phylum Bacteroidetes | 20 | This study |
| Fibr225 (00005) | 16S | Fibrobacter succinogenes-related clones, phylum Fibrobacteres | 20c | 16 |
| ARCH915 (00027) | 16S | Domain Archaea | 20 | 16 |
a
The numbers in parentheses after the probe names represent the probe accession numbers in probeBase (16).
b
FA, formamide concentration used in the FISH buffer.
c
The optimum formamide concentration for the probe was determined in this study.