Due to continuous improvements in the FISH technique, it is now a very useful tool for studies in microbiology. Knowledge of the compositions and distributions of microorganisms in natural habitats plays a key role in safety and technological aspects of food microbiology. FISH can be used directly in the sample studied as a relatively rapid culture-independent method in order to evaluate the presence and activity of pathogens or other undesirable microorganisms. Moreover, molecular cytogenetics is a valid approach for studying the activity of bacteria involved in technological processes (e.g., food fermentation) or that are important for promoting human health. In this chapter, we present an overview of FISH protocols for the microbiological analysis of food.
