TABLE 1.

Probes and conditions used to estimate abundance of bacterial groups in fermentor samples

ProbeSequence (5′-3′)Probe targetValidationaHybridization temp (°C)Formamide concn (%)Source or reference
Eub338GCTGCCTCCCGTAGGAGTDomain BacteriaAll strains listed here5001
Erec482GCTTCTTAGTCAGGTACCGClostridial clusters XIVa+bE. hallii L2-7, Coprococcus sp. strain L2-50; E. rectale A1-86, R. intestinalis L1-8247016
Bac303CCAATGTGGGGGACCTTBacteroides-Prevotella groupB. vulgatus BV1447, B. thetaiotaomicron B5482, B. distasonis DSM 2070147040
Fprau645CCTCTGCACTACTCAAGAAAAACF. prausnitzii groupF. prausnitzii A2-16550050
Bif164CATCCGGCATTACCACCCBifidobacterium genusB. adoloscentis L2-32, B. longum NCIMB 8809, B. infantis DSM 2008850030
Rfla729AAAGCCCAGTAAGCCGCCR. flavefaciens subclusterR. albus SY3, R. flavefaciens 17 R. bromii L2-63502020
Rbro730TAAAGCCCAG(C/T)AGGCCGCR. bromii subcluster502020
Rrec584TCAGACTTGCCG(C/T)ACCGCRoseburia genusE. rectale A1-86, R. intestinalis L1-82500This study
Lab158GGTATTAGCA(C/T)CTGTTTCCALactobacillus-Enterococcus groupL. acidophilus A2-74, E. faecalis JH2-2472019
Ato291GGTCGGTCTCTCAACCCAtopobium clusterC. aerofaciens DSM 397950021
Prop853ATTGCGTTAACTCCGGCACClostridial cluster IXM. elsdenii LC1500This study
Enterobact DTGCTCTCGCGAGGTCGCTTCTCTTEnterobacteriaceaeE. coli MG165550044
  • a That is, a positive reaction was seen.