TABLE 2.

Panel of group- and species-specific 16S rRNA-targeted oligonucleotide probes

TargetProbeSequence (5′ to 3′)cOPD codeaReference
Domain BacteriaEUB 338GCTGCCTCCCGTAGGAGTS-D-Bact-0338-a-A-18 1
NON 338ACATCCTACGGGAGGCNAb 45
Bacteroides-Prevotella Bac 303CCAATGTGGGGGACCTTS-*-Bacto-0303-a-A-17 28
Bacteroides putredinis Bputre 698GTTCTGTATGATCTCTAAGCS-S-Bputr-0698-a-A-20 37
Bacteroides vulgatus Bvulg 1017AGATGCCTTGCGGCTTACGGCS-S-Bvulg-1017-a-A-21 37
EnterobacteriaEnter 1432CTTTTGCAACCCACTS-*-Ent-1432-a-A-15 41
Lactobacillus-Streptococcus groupLab 158GGTATTAGCAYCTGTTTCCAS-G-Lab-0158-a-A-20 14
Bifidobacterium groupBif 164CATCCGGCATTACCACCCS-G-Bif-0164-a-A-18 25
Atopobium clusterAto 291GGTCGGTCTCTCAACCCS-*-Ato-0291-a-A-17 16
Clostridium coccoides-Eubacterium rectale clusterErec 482GCTTCTTAGTCARGTACCGS-*-Erec-0482-a-A-19 12
Faecalibacterium prausnitzii clusterFprau 645CCTCTGCACTACTCAAGAAAAACS-*-Fprau-0645-a-A-23 43
Ruminococcus groupRbro 730TAAAGCCCAGYAGGCCGCS-*-Rbro-0730-a-A-18 15
cpRbro1dTAAAGCCCAGYAAGCCGC 26
cpRbro2d GGT GCCCAGYAGGCCGC 26
Clostridium viride groupCvir 1414GGGTGTTCCCGRCTCTCAS-*-Cvir-1414-a-A-18 26
cpCvir1dGGGTGTTDCCGRCTCTCA 26
cpCvir2dGGGTGTTCCCGRCTTTCA 26
cpCvir3dGGGTCCCCCCGRCTCTCA 26
Eubacterium cylindroides subgroupEcyl 387CGCGGCATTGCTCGTTCAS-*-Ecyl-0387-a-A-18 15
Streptococcus-Lactococcus groupStrc 493GTTAGCCGTCCCTTTCTGGS-*-Strc-0493-a-A-19 12
cpStrcd T TTAGCCGTCCCTTTCTGG 26
Clostridium ramosum assemblageCra 757CCACGCTTTCGKGAMTGAS-S-Cra-0757-a-A-18 26
cpCradCCACGCTTTCGKGAMTCA 26
  • a OPD code, oligonucleotide probe database code.

  • b NA, not applicable.

  • c Sequence in IUPAC code: R = G/A, Y = T/C, M = A/C, K = G/T, S = G/C, W = A/T, H = A/C/T, B = G/T/C, V = G/C/A, D = G/A/T, N = G/A/T/C.

  • d Competitor oligonucleotide probe.