Table 1. Probes used for bacterial enumeration by FISH.

Probe name	Sequence (5’ to 3’)	Target species	Hybridization- Washing Temperature (°C)	Reference
Ato291	GGTCGGTCTCTCAACCC	Atopobium, Colinsella, Olsenella and Eggerthella spp.; Cryptobacterium curtum; Mycoplasma equigenitalium and Mycoplasma elephantis	50 - 50	[54]
Bac303	CCAATGTGGGGGACCTT	Most Bacteroides sensu stricto and Prevotella spp.; all Parabacteroides; Barnesiella viscericola and Odoribacter splanchnicus	46 - 48	[55]
Bif164	CATCCGGCATTACCACCC	Most Bifidobacterium spp. and Parascardovia denticolens	50 - 50	[56]
Chis150	TTATGCGGTATTAATCTYCCTTT	Most members of Clostridium cluster I; all members of Clostridium cluster II; Clostridium tyrobutyricum; Adhaeribacter aquaticus and Flexibacter canadensis (family Flexibacteriaceae); [Eubacterium] combesii (family Propionibacteriaceae)	50 - 50	[57]
Erec482	GCTTCTTAGTCARGTACCG	Most members of Clostridium cluster XIVa; Syntrophococcus sucromutans, [Bacteroides] galacturonicus and [Bacteroides] xylanolyticus, Lachnospira pectinschiza and Clostridium saccharolyticum	50 - 50	[57]
Lab158	GGTATTAGCAYCTGTTTCCA	Most Lactobacillus, Leuconostoc and Weissella spp.; Lactococcus lactis; all Vagococcus, Enterococcus, Melisococcus, Tetragenococcus, Catellicoccus, Pediococcus and Paralactobacillus spp.	50 - 50	[58]
Rrec584	TCAGACTTGCCGYACCGC	Roseburia - Eubacterium rectale (a component of cluster XIVa)	50 - 50	[59]
Eco1531	CACCGTAGTGCCTCGTCATC	Escherichia coli	37 - 37	[59]
EUB338	GCTGCCTCCCGTAGGAGT	Total bacteria	46 - 48	[60]
EUB338II	GCAGCCACCCGTAGGTGT	Total bacteria	46 - 48	[60]
EUB338II	GCTGCCACCCGTAGGTGT	Total bacteria	46 - 48	[60]