Table 1

 FISH probes

NameTargetReference
Formamide concentration and hybridisation temperature were chosen to achieve the optimum stringency as described in the references for each probe set. Additional hybridisations using a permeation step with lysozyme for 15, 30 and 60 min were performed in parallel for detection of Gram-positive bacteria.
Eub338Virtually all bacteria, Kingdom Eubacteria 7
Gamma-proteobacteria
    Aer66 Aeromonas 8
    EbacEnterobacteriaceae 9
    Ec1531 Escherichia coli 10
    Haeinf Haemophilus influenzae 11
    Stemal Stenotrophomonas maltophilia 11
    Ps Pseudomonas 12
    Pseaer A Pseudomonas aeruginosa 11
    Pseaer B Pseudomonas aeruginosa 11
    AcAc Actinobacillus actinomycetemcomitans 13
Beta-proteobacteria
    Bet42aBeta-proteobacteria incl Neisseria 14
    Burkho Burkholderia 11
    Burcep Burkholderia cepacia 11
Epsilon-proteobacteria
    Arc1430Arcobacter, Epsilon-proteobacteria 15
    Hpy-1Helicobacter pylori, Epsilon-proteobacteria 16
Firmicutes
    LGC Firmicutes 17
    Erec482Clostridium coccoides - Eubacterium rectale group 18
    LachSubgroup of Erec (incl. Lachnospira multipara) 19
    Chis150Clostridium histolyticum group 18
    Clit135Clostridium lituseburense group (incl. Clostridiumdifficile) 18
    Ehalsubgroup of Erec (incl. Eubacterium hallii) 19
    EcylEubacterium cylindroides and others 19
    EfaecEnterococcus faecalis, Enterococcus sulfuricus 20
    Strc493Streptococcus group 18
    Lab158Lactobacillus and Enterococcus group 21
    Strpyo Streptococcus pyogenes 11
    Enc131 Enterococcus 22
    Staaur Staphylococcus aureus 11
    VeilVeillonella group 19
    Vepa Veillonella parvula 13
    FprauFusobacterium prausnitzii group 23
    SfbSegmented filamentous bacteria 24
    Lis 637,1255 Listeria, Brochothrix 25
    UroA, UroBRuminococcusobeum-like bacteria (subgroup of Erec) 26
    PhascoPhascolarctobacterium faecium group 19
    Rbro, RflaRuminococcus bromii, Ruminococcus flavefaciens and others 19
Actinobacteria
    HGC Actinobacterium 27
    Cor653 Coriobacterium 28
    Ato291Atopobium, Coriobacterium, Eggerthella and Collinsella 28
    Bif164, 662Bifidobacteriaceae 29
Cytophaga-Flavobacterium-Bacteroides
    Bac303 Bacteroides/Prevotella 30
    CF319aCytophaga-Flavobacteria 30
    Bdis656 Bacteroides distasonis 18
    Bfra Bacteroides fragilis 18
    Prin Prevotella intermedia 13
    Pogi Porphyromonas gingivalis 13
    B(T)AFO Tannerella forsythia 13
Spirochaetes
    Ser1410 Brachyspira 31
    Borr4 Borrelia 32
Fusobacteria
    FusoFusobacterium spp 13
    Non338Nonsense probe used to test for non-specific binding 14