Development of a real-time PCR-based system targeting the 16S rRNA gene sequence for rapid detection of Alicyclobacillus spp. in juice products

The thermophilic, aciduric Alicyclobacillus spp. are becoming an increasing spoilage concern in the beverage industry. Rapid methods to detect their presence in both raw materials and final products are desirable for industrial quality control. The objective of this study was to develop a real-time TaqMan®-based polymerase chain reaction (PCR) system for rapid and specific detection of thermophilic spoilage bacteria, mainly Alicyclobacillus spp., for food industry applications. Two primers and a fluorogenic probe targeting 16S rRNA encoding gene sequences, capable of detecting the genus Alicyclobacillus and a few other closely related thermophiles, were developed, and the efficiency of the detection system was evaluated in both bacterial medium and juice products. Using this system, the presence of less than 100 Alicyclobacillus cells could be detected without cross-reactivity with other common food-borne bacteria.