title: Application of FISH technology for microbiological analysis: current state and prospects.
abstract: In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.
authors.affiliation: Department of Genetic, Biology of Microorganisms, Anthropology, Evolution, University of Parma, via Usberti 11/A, 43100 Parma, Italy. benedetta.bottari@nemo.unipr.it
authors.forename: Benedetta
authors.initials: B
authors.lastname: Bottari
authors.forename: Danilo
authors.initials: D
authors.lastname: Ercolini
authors.forename: Monica
authors.initials: M
authors.lastname: Gatti
authors.forename: Erasmo
authors.initials: E
authors.lastname: Neviani
mesh_terms: D001419:Bacteria; D015373:Bacterial Typing Techniques; D018441:Biofilms; D005516:Food Microbiology; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D015336:Molecular Probe Techniques; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012335:RNA, Ribosomal