TABLE 2.

FISH probesa

Probe nameTargetReference
Eub338Virtually all bacteria, kingdom Bacteria (Eubacteria)1
Alf1bAlpha subclass of class Proteobacteria20
Beta42aBeta subclass of class Proteobacteria20
Gam42aGamma subclass of class Proteobacteria (including Enterobacteriaceae)20
EbacEnterobacteriaceae4
Ec1531Escherichia coli26
Y16s-69Yersinia species32
Srb385Sulfate-reducing bacteria2
Hpy-1Helicobacter pylori epsilon subclass of Proteobacteria8
Arc1430Arcobacter sp. epsilon subclass of Proteobacteria29
HGCClass Actinobacteria (gram-positive bacteria with high G + C contents)27
LGCFirmicutes (gram-positive bacteria with low G + C contents)24
SfbSegmented filamentous bacteria33
Erec482Eubacterium rectale-Clostridium coccoides group11
LachSubgroup (including Lachnospira multipara)14
EhalSubgroup (including Eubacterium hallii)14
Chis150Clostridium histolyticum group11
Clit135Clostridium lituseburense group (including Clostridium difficile)11
Lab158Lactobacillus and Enterococcus group12
Strc493Streptococcus group11
Enc131Enterococcus spp. and other10
EfaecEnterococcus faecalis, Enterococcus sulfuricus15
Ato291Atopobium, Coriobacterium, Eggerthella, and Collinsella spp.13
Cor653Coriobacterium group13
EcylEubacterium cylindroides and other14
PhascoPhascolarctobacterium faecium group14
VeilVeillonella group14
Rbro, RflaRuminococcus bromii, Ruminococcus flavefaciens, and other14
UroA, UroBRuminococcus obeum-like bacteria (subgroup of Eubacterium rectale)35
Ser1410Genus Brachyspira16
Bif164Bifidobacterium18
CF319aCytophaga-Flavobacteria group21
Bac303Bacteroides-Prevotella group21
Bfra602Bacteroides fragilis group11
Bdis656Bacteroides distasonis group11
FprauFusobacterium prausnitzii group30
Arch915Archaea20
Non338Nonsense probe used to test for nonspecific binding20
  • a The formamide concentration and hybridization temperature were chosen to achieve the optimal stringency, as described in the references. Additional hybridizations by use of a permeation step with lysozyme for 15, 30, and 60 min were performed in parallel for detection of gram-positive bacteria. For convenience, the numbers within the probe name that identify the location of the probe sequence within the ribosomal RNA genes are not repeated in the text.