Fluorescent In Situ Hybridization technique (FISH) is based on the hybridization of fluorescent labeled oligonucleotide probe to a specific complementary DNA or RNA sequence in whole and intact cells.1 Microbial FISH allows the visualization, identification and isolation of bacteria due to recognition of ribosomal RNA also in unculturable samples.2
FISH technique can serve as a powerful tool in the microbiome research field by allowing the observation of native microbial populations in diverse microbiome environments, such as samples from human origin (blood3 and tissue4), microbial ecology (solid biofilms5 and aquatic systems 6) and plants7. It is strongly recommended to include positive and negative controls in FISH assays to ensure specific binding of the probe of interest and appropriate protocol conditions. We offer positive (MBD0032/33) and negative control (MBD0034/35) probes, that accompany the specific probe of interest.
Escherichia coli is a gram negative, facultative aerobic, rod-shaped coliform bacterium. E. coli colonizes the infant gut within hours of birth and establishes itself as the most abundant facultative anaerobe of the human intestinal microflora for the remainder of life, equipped with the abilities to grow in the ever-changing environment in the gut and cope with the mammalian host interaction.8,9 Nevertheless, E. coli can survive in many different ecological habitats, including abiotic environments, and is considered a highly versatile species. Known habitats of E. coli include soil, water, sediment, and food. Some strains of E. coli have evolved and adapted to a pathogenic lifestyle and can cause different disease pathologies.10
Escherichia coli probe specifically recognizes Escherichia coli cells.
Yet there are some reports that describe recognition of other bacteria with this probe, such as, Shigella boydii, Citrobacter davisae, Citrobacter lapagei, Citrobacter neteri 11 and Klebsiella pneumoniae 12.
FISH technique was successfully used to identify E.coli with the probe in various samples such as pure culture (as described in the figure legends and11,13), large and small intestines samples14-16, fecal samples17-21, colonic biopsies18, urine samples, bladder and kidney sections embedded in paraffin22 and in E.coli biofilm23.