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Methods for the identification of probiotic bacteria in foods are discussed including a number of molecular-based techniques. Aspects considered include: German guidelines relating to the use of probiotic cultures in foods; nomenclature used to describe probiotic bacteria; identification problems which have occurred within different classification groups (Lactobacillus acidophilus, L. casei, L. reuteri/L. fermentum, bifidobacteria); workload and precision of methods used to identify probiotic cultures; and the need for further in depth information about various probiotic bacterial strains.