TABLE 1.
16S rRNA oligonucleotide probes used for hybridization
| Probe | Specificity | Sequence of probe (5′–3′) | Target sitea | FA (%)b | Reference or source |
|---|---|---|---|---|---|
| Univ1392 | All life | ACGGGCGGTGTGTRC | 16S (1392) | NAe | 47 |
| Eub338 | Bacteria | GCTGCCTCCCGTAGGAGT | 16S (338) | 0 | 2 |
| Alphalb | α Proteobacteria | CGTTCGYTCTGAGCCAG | 16S (19) | 20 | 32 |
| Beta42a | β Proteobacteria | GCCTTCCCACTTCGTTT | 23S (1027) | 35 | 32 |
| Gam42A | γ Proteobacteria | GCCTTCCCACATCGTTT | 23S (1027) | 35 | 32 |
| CF319A | CFB phylum | TGGTCCGTGTCTCAGTAC | 16S (319) | 35 | 33 |
| HGC69a | Gram-positive bacteria with high G+C content | TATAGTTACCACCGCGT | 23S (1901) | 25 | 38 |
| LGC344A | Gram-positive bacteia with low G+C content | TGGAAGATTCCCTACTGC | 16S (354) | 20 | 34 |
| LGC354B | Same as LGC354A | CGGAAGATTCCCTACTGC | |||
| LGC354C | Same as LGC354A | CCGAAGATTCCCTACTGC | |||
| SRB385 | δ Proteobacteria | CGGCGTCGCTGCGTCAGG | 16S (385) | 35 | 1 |
| VM338c | Verrucomicrobia | TGCTGCCACCCGTAGGTG | 16S (338) | 50 | This study |
| IRog1 | Acidobacterium-Holophaga phylum | AAGGCGGCATCCTGGACC | 16S (353) | 35 | 31 |
| IRog2 | Acidobacterium-Halophaga phylum | GCAGTGGGGAATTGTTC | 16S (728) | ||
| Clost I | Clostridial cluster I | TTCTTCCTAATCTCTACGCA | 16S (696) | 30 | 26 |
| Clost III | 7 sequences of clostridial cluster III; strains FCB90-1 FCB90-2 FCB45, and RCel1 from rice soild | CCTGTGTTATCCCCCTGT | 16S (140) | 30 | This study |
| Clost IV | Clostridial cluster IV, some members of the genera Eubacterium, Rhodothermus, and Chlorobium | GCACCCTTTACACCC | 16S (565) | 30 | This study |
| Clost XIVa | 25 isolates form cluster XIVa of the genus Clustridum | CTGTATGAGGCAGGT | 16S (129) | 30 | This study |
| Clost XIVa-c | 16S rRNA clones related to cluster XIVa but nto detectable with probe clost XIVa; three isolates of cluster XIVa | CAGCTGTTATCCCCCTGTAT | 16S (138) | 40 | This study |
| Clost XIVa- amino | 3 isolates of cluster XIVa | GTACCATGCGGCACT | 16S (183) | 40 | This study |