5 Bacteriophages in Dairy Industry: PCR Methods as Valuable Tools Beatriz del Río, María Cruz Martín, Víctor Ladero, Noelia Martínez, Daniel M. Linares, María Fernández and Miguel A. Alvarez Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Spain 1. Introduction Microorganisms have been empirically used since ancestral times to produce fermented dairy products from milk. In the actual dairy industry, milk is subjected to large scale fermentation processes that involve microorganisms mostly belonging to the Lactic Acid Bacteria (LAB) group. Bacteriophages that infect LAB have been claimed as one of the principal sources of fermentation failure (spoilage or delay) on the manufacture of many dairy products (Brüssow et al., 1998; Josephsen & Neve, 1998; Garneau & Moineau, 2011). Some estimates assume that virulent phages are the primary direct responsible of the largest-economic loss of dairy factories, since they affect negatively up to the 10% of all milk fermentations (Moineau & Levesque, 2005). Starter cultures consisting in selected bacterial strains are added to the fermentation vats to enhance the fermentative process and also to improve or influence the flavor and texture of the cultured products. The starter culture population grows through the fermentation process and reaches high levels inside the industrial vat. This is the perfect environment where bacteriophages can infect sensitive bacteria. The lysis of the infected host-bacteria can decrease several folds the total number of starter cells with consequences ranging from the delay of the acidification with quality changes of the final product, to the total failure of the fermentation. Even with frequent cleaning, disinfestations and sterilization of all the facilities, the total absence of phages in the dairy plants is a utopia. The number and types of phages that are introduced within the system, presumably as a consequence of the constant supply of wild phages, is very variable and different subpopulations can prevalence as soon as a susceptible strain is introduced in the fermentation scheme (Neve et al., 1995; Bruttin et al., 1997; Chibani-Chennoufi et al., 2004; Kleppen et al., 2011). In fact, bacteriophages have been detected in variable titer in the milk, appliances of the factory, additives and starter cultures. Since dairy bacteriophages are one of the mayor dairy threats, great research efforts have been made to reduce its load on dairy plants and to design new monitoring methods for their early detection (Magadán et al., 2009; Garneau & Moineau, 2011). Classical microbiological assays are routinely used on dairy plants to test the presence of bacteriophages. The spot/plaque assay and the turbidity/growth test are the two methods