TABLE 1.

Partial 16S rRNA gene sequences of reference organisms with group-specific primers

Organism or siteaForward primerReverse primer
DesignationSequencebDesignationSequenceb
C. leptum subgroup-specific primerssg-Clept-F5′ GCACAAGCAGTGGAGT 3′sg-Clept-R33′ AACTGTTTTGCCTCCTTC 5′
    Target site5′ GCACAAGCAGTGGAGT 3′5′ TTGACAAAACGGAGGAAG 3′
    Clostridium cellulosic.....................T.............
    Clostridium leptumc...................................
    Clostridium orbiscindensc........G..........................
    Clostridium sporosphaeroidesc........N..........................
    Clostridium viridec........G..........................
    Eubacterium desmolansc...................................
    Eubacterium siraeumc...................................
    Faecalibacterium prausnitziic...................................
    Ruminococcus albusc...................................
    Ruminococcus bromiic...................................
    Ruminococcus callidusc...................................
    Ruminococcus flavefaciensc...................................
    Clostridium coccoides........G.......C.GG..TN.CC........
    Bifidobacterium longum........G.C.....C.GG.TT..CT........
    Collinsella aerofaciens..........C.....C.CC.T...GG-.....G.
    Bacteroides vulgatus........G.A.....C..C.TA.G.TGT......
Atopobium cluster-specific primersc-Atopo-F5′ GGGTTGAGAGACCGACC 3′c-Atopo-R3′ GGACGTCTTCTTCGRGGC 5′
    Target site5′ GGGTTGAGAGACCGACC 3′5′ CCTGCAGAAGAAGCYCCG 3′
    Atopobium minutumc...................................
    Atopobium fossorc...................................
    Atopobium rimaec...................................
    Atopobium parvulumc...................................
    Collinsella aerofaciensc...................................
    Collinsella intestinalisc...................................
    Collinsella stercorisc...................................
    Coriobacterium sp. strain EKSO3c...................................
    Coriobacterium glomeransc................A..................
    Eggerthella lentac...................................
    Cryptobacterium curtumc...................................
    Slackia heliotrin reducens...C......G.T...T..................
    Denitrobacterium detoxificans..AC......GT....T..................
    Bifidobacterium longum..CC......GG.......C.TT...T....A...
    Bacteroides vulgatus.TTC......GAA..GT.T.TAT...T...GAT..
    Clostridium coccoides..CC......GGT...A....ACTN..........
    Faecalibacterium prausnitzii..AC......GTT...A.TCAACA.G....TGA..
  • a The positions of the target sites for the primers are as follows (numbering based on the Escherichia coli 16S rRNA gene sequence): sg-Clept-F, nucleotides 933 to 948; sg-Clept-R3, nucleotides 1164 to 1181; c-Atopo-F, nucleotides 292 to 308; and g-Atopo-R, nucleotides 488 to 505.

  • b Only nucleotides that differ from nucleotides in the target sequences are shown.

  • c Targeted organism.