Spoilage is a serious problem for the food industry because it renders products unacceptable for consumption. Spoilage of foods and feeds is often the result of microbial activity from a variety of organisms. The microbial flora that will develop depends very much on both intrinsic and extrinsic parameters, modes of processing and preservation, and implicit parameters (Deak 1991; Van der Vossen and Hofstra 1996). Yeasts and moulds can be found in a variety of environments because they can utilize a variety of substrates, and are relatively tolerant to low pH, low water activity, low temperature and preservatives. Consequently, although only a limited range of fungal species are responsible for the spoilage of a given food (Filtenborg et al. 1996), contamination of foods and feeds by yeasts and moulds has been extensively reported (Huis in't Veld 1996). Fungi can contaminate foods and feeds at different stages including harvesting, processing and handling. Changes induced by spoilage of yeasts and moulds can be of a sensory nature, e.g., production of slime, pigmented growth, discoloration, rotting, development of off-odors and off-flavors. The most important aspect of food spoilage is, however, the formation of mycotoxins that may cause food poisonings. Although traditional morphological and physiological characters are fundamental parameters contributing to the identification of microorganisms in foods and feeds, these criteria may be influenced by environmental conditions. To supplement classical methods, a number of nucleic acid-based methods have been developed in the past few years. These methods have the advantage over phenotypic methods of not being influenced by environmental conditions of the cells since the nucleotide sequence of DNA remains constant during growth. This review focuses on molecular methods developed for direct detection of fungi in different foods and feeds. First, we will discuss two basic types of detection methods, those based on DNA hybridization, and those based on DNA amplification. In the second part of the chapter, the possible nucleic acid targets of direct detection methods will be discussed.

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