The present invention provides formulations and methods for isolating food-borne pathogens from a great variety of food matrices. Methods for isolating microorganisms from clinical and environmental specimens are also disclosed. The invention also concerns methods for rapid and efficient isolation of sufficiently pure DNA from small amounts of various pathogenic microorganisms, which then can be used, according to the methods of the instant invention, for selective identification of a live pathogenic microorganism present in a sample from which the microorganism was isolated. The methods of the instant invention are also useful for identification of new pathogenic microorganisms, diagnostics of food-borne illnesses, treatment of food-borne diseases and quality control of food items offered for sale to consumers.