title: Histo-FISH protocol to detect bacterial compositions and biofilms formation in vivo.
abstract: The study of biofilm function in vivo in various niches of the gastrointestinal tract (GIT) is rather limited. It is more frequently used in in vitro approaches, as an alternative to the studies focused on formation mechanisms and function of biofilms, which do not represent the actual in vivo complexity of microbial structures. Additionally, in vitro tests can sometimes lead to unreliable results. The goal of this study was to develop a simple approach to detect bacterial populations, particularly Lactobacillus and Bifidobacterium in biofilms, in vivo by the fluorescent in situ hybridisation (FISH) method. We standardised a new Histo-FISH method based on specific fluorochrome labelling probes which are able to detect Lactobacillus spp. and Bifidobacterium spp. within biofilms on the mucosal surface of the GIT embedded in paraffin in histological slices. This method is also suitable for visualisation of bacterial populations in the GIT internal content. Depending on the labelling probes, the Histo-FISH method has the potential to detect other probiotic strains or pathogenic bacteria. This original approach permits us to analyse bacterial colonisation processes as well as biofilm formation in stomach and caecum of BALB/c and germ-free mice.
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: M
authors.initials: M
authors.lastname: Madar
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: M
authors.initials: M
authors.lastname: Slizova
authors.affiliation: 2 The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jablonna, Poland.
authors.forename: J
authors.initials: J
authors.lastname: Czerwinski
authors.affiliation: 3 Parasitological Institute Slovak Academy of Science, Hlinkova 3, 04001 Kosice, Slovakia.
authors.forename: G
authors.initials: G
authors.lastname: Hrckova
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: D
authors.initials: D
authors.lastname: Mudronova
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: S
authors.initials: S
authors.lastname: Gancarcikova
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: M
authors.initials: M
authors.lastname: Popper
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: J
authors.initials: J
authors.lastname: Pistl
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.|3 Parasitological Institute Slovak Academy of Science, Hlinkova 3, 04001 Kosice, Slovakia.
authors.forename: J
authors.initials: J
authors.lastname: Soltys
authors.affiliation: 1 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia.
authors.forename: R
authors.initials: R
authors.lastname: Nemcova
mesh_terms: D000818:Animals; D001644:Bifidobacterium / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D018441:Biofilms / Q000254:growth & development*; D005856:Germ-Free Life; D006651:Histocytochemistry / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D007413:Intestinal Mucosa / Q000382:microbiology*; D007778:Lactobacillus / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D008807:Mice, Inbred BALB C
keywords: Bifidobacterium spp.; FISH; Lactobacillus spp.; colonisation; gastrointestinal tract