TABLE 1.
Probes and conditions used to estimate abundance of bacterial groups in fermentor samples
| Probe | Sequence (5′-3′) | Probe target | Validationa | Hybridization temp (°C) | Formamide concn (%) | Source or reference |
|---|---|---|---|---|---|---|
| Eub338 | GCTGCCTCCCGTAGGAGT | Domain Bacteria | All strains listed here | 50 | 0 | 1 |
| Erec482 | GCTTCTTAGTCAGGTACCG | Clostridial clusters XIVa+b | E. hallii L2-7, Coprococcus sp. strain L2-50; E. rectale A1-86, R. intestinalis L1-82 | 47 | 0 | 16 |
| Bac303 | CCAATGTGGGGGACCTT | Bacteroides-Prevotella group | B. vulgatus BV1447, B. thetaiotaomicron B5482, B. distasonis DSM 20701 | 47 | 0 | 40 |
| Fprau645 | CCTCTGCACTACTCAAGAAAAAC | F. prausnitzii group | F. prausnitzii A2-165 | 50 | 0 | 50 |
| Bif164 | CATCCGGCATTACCACCC | Bifidobacterium genus | B. adoloscentis L2-32, B. longum NCIMB 8809, B. infantis DSM 20088 | 50 | 0 | 30 |
| Rfla729 | AAAGCCCAGTAAGCCGCC | R. flavefaciens subcluster | R. albus SY3, R. flavefaciens 17 R. bromii L2-63 | 50 | 20 | 20 |
| Rbro730 | TAAAGCCCAG(C/T)AGGCCGC | R. bromii subcluster | 50 | 20 | 20 | |
| Rrec584 | TCAGACTTGCCG(C/T)ACCGC | Roseburia genus | E. rectale A1-86, R. intestinalis L1-82 | 50 | 0 | This study |
| Lab158 | GGTATTAGCA(C/T)CTGTTTCCA | Lactobacillus-Enterococcus group | L. acidophilus A2-74, E. faecalis JH2-2 | 47 | 20 | 19 |
| Ato291 | GGTCGGTCTCTCAACCC | Atopobium cluster | C. aerofaciens DSM 3979 | 50 | 0 | 21 |
| Prop853 | ATTGCGTTAACTCCGGCAC | Clostridial cluster IX | M. elsdenii LC1 | 50 | 0 | This study |
| Enterobact D | TGCTCTCGCGAGGTCGCTTCTCTT | Enterobacteriaceae | E. coli MG1655 | 50 | 0 | 44 |
a
That is, a positive reaction was seen.