TABLE 1.

16S rRNA-targeted oligonucleotide probes used in microchip analyses

Probe no.Target organism(s)Probe sequenceDesignation of probeaSource or reference
4Methanobacterium [other than strains reacting with Mb(II)Mbt 1285]5′-CGAACTACGACCTGGTTTAG-3′Mb(I) 643This work
5M. thermoautotrophicum, M. wolfei, M. thermaggregans, Methanothermobacter5′-CCCGGCCTCAAGCCTAATAG-3′Mb(II)Mbt 1285This work
6Thermococcus + Pyrococcus5′-ACTTACGGGCCCGGCTACGG-3′TcPc 579This work
21Geotoga5′-AGTTTCATGCGCACTGACAC-3′Got 625This work
25Petrotoga5′-CTGTAGTGTGTCCACTACCC-3′Pet 454This work
27Petrotoga5′-GCCCAGTAGACCAACTTCTT-3′Pet 725This work
30Thermococcus5′-CCAGTACCTCAGGCCTAT-3′Tc 179This work
39Thermodesulfobacterium5′-TAACCTATGACTTGTCCAGC-3′Tdb 588This work
44Desulfurococcus5′-TCGACCCGACCCAAGGGGCC-3′Dco 1440This work
46Desulfotomaculum (D. geothermicum, D. thermobenzoicum, D. australicum)5′-GCGGACCCATCCATTAGCGG-3′Dfm(I) 218This work
48Desulfotomaculum (D. ruminis, D. nigrificans)5′-AAGTCCACCAGTATCAGAGG-3′Dfm(II) 634This work
50Thermoanaerobacter5′-CTCGCTACTACCTGCATGTC-3′Tab 993This work
52Thermus (T. thermophilus, T. flavus, T. aquaticus, but not T. filiformis and T. scotoductus)5′-GGGTTTCGTCCCGGGTTC-3′S-G-Thus-0438-a-A-1818
53Geobacillus5′-GGGTGTGACCCCTCTAAC-3′S-*-Tbcil-0832-a-A-1818
54Thermotoga + Thermosipho5′-GTTCCGTCTCCCTCTACC-3′S-*-Ttoga-0660-a-A-1818
55Aquificales + Desulfurobacterium and Thermovibrio species5′-TCGCGCAACGCTCGGGACC-3′S-O-Hydr-0540-a-A-1918
58Methanobacterium (all species) + Methanothermobacter5′-CCACCCCGTTAAGAGTG-3′MbMbt 408This work
  • a The designations of the probes published earlier (17) are according to the Oligonucleotide Probe Database nomenclature (2). The designations of the probes designed in the present work include generic abbreviations adopted in the Ribosomal Database Project (27) and the target position in E. coli numbering.