TABLE 1.

Probes used during the study

Probe nameOPD nameaTarget species with zero mismatchesProbe sequence 5′-3′TH (°C)Reference or source
Species-specific probes
    A. caccaeS-S-Acac-0194-a-A-18A. caccaeCTA TAC TGC CAG GGC TTT46This study
    R. intestinalisS-S-Rint-1102-a-A-18R. intestinalisGCT TAC CCG CTG GCT ACT46This study
    Eubacterium sp. strain L1-83bS-St-xxxx-0576-a-A-18Eubacterium sp. strains L1-83 and A2-194AGC CTT CCG CCT GCG CTC58This study
    Coprococcus sp. strain L2-50bS-St-xxxx-0060-a-A-18Coprococcus sp. strain L2-50CAC CGA TCT TCT CTC GTT54This study
    E. rectale sp. strain A1-86bS-S-Erec-0207-a-A-18E. rectale strain A1-86GGT GGT GTA CAA GAC CCG52This study
    E. barkeriS-S-Ebar-1237-a-A-18E. barkeri, E. aggregansCCT TTG TCC CAA CCC ATT5122
    E. biformeS-S-Ebif-0462-a-A-18E. biformeCAC TCA CTC ATC ATT CCC5122
    E. cylindroidesS-St-Ecyl-0461-a-A-18E. cylindroidesACC CAC GGA TCA TTC CCT5122
    E. cylindroidesS-St-Ecyl-0466-a-A-18E. cylindroidesCCG TCA CCC ACA TAG CAT5122
    E. hadrumS-*-Ehad-0579-a-A-20E. hadrumGAC TTG CCA TAC CAC CTA CG5422
    E. limosumS-*-Elim-1433-a-A-18E. callanderi, E. limosumGCG GTT CTC TCA CAG GCT5122
    E. moniliformeS-S-Emon-0084-a-A-18E. moniliformeCCG CTA ATC CAT TTC CCG5123
    E. multiformeS-S-Emul-0183-a-A-18E. multiformeGTT CCT TCA TGC GAA GGT5123
    E. ramulusS-S-Eram-0997-a-A-18E. ramulusACA TGT TCT GTC ACC GGG4624
    E. saburreumS-S-Esab-1467-a-A-18E. saburreumAGT TAT CCT CCC TGC CTT4823
    E. ventriosumS-S-Even-0066-a-A-18E. ventriosumTCT GTC CAA GGT GCT TCG5522
Group-and cluster-specific probes
    E. hallii L2-7/ E. halliiS-*-Ehal-0578-a-A-18E. hallii L2-7, E. halliiTTG CAC TGC CAC CTA CGC58This study
    E. cylindroides clusterS-*-Ecyl-0387-a-A-18C. innocuum, E. biforme, E. cylindroides, E. dolichum, E. tortuosum, Streptococcus pleomorphusCGC GGC ATT GCT CGT TCA4611
    Ruminococcus-Eubacterium-Clostridium clusterS-*-Erec-0482-a-A-19For details see Franks et al. (10)GCT TCT TAG TCA RGT ACC G5010
    C. eutactusS-*-Ceut-0705-a-A-21C. eutactus, Coprococcus sp. strain L2-50GTC AGT AGC AGT CCA GTA AGT54This study
    F. prausnitziiS-*-Fpra-0655-a-A-18F. prausnitzii A2-165 and L2-6CGC CTA CCT CTG CAC TAC58This study
    R. intestinalis subclusterS-*-Rint-0623-a-A-18Eubacterium sp. strains L1-83 and A2-194, E. rectale sp. strains A1-86, T1-815, and Roseburig sp. strain A2-183, and R. cecicola, R. intestinalis, E. rectale, E. ramulusTTC CAA TGC AGT ACC GGG54This study
    C. histolyticumS-*-Chis150-a-A-23For details see Franks et al. (10)TTA TGC GGT ATT AAT CTY CCT TT5010
    C. lituseburenseS-*-Clit135-a-A-19For details see Franks et al. (10)GTT ATC CGT GTG TAC AGG G5010
  • a Standardized probe name in accordance with the OPD (1).

  • b No valid systematic name was available.