Impact of bacterial genomics on determining quality and safety in the dairy production chain

Genomics is revolutionizing our understanding of biological systems and is providing new opportunities for the dairy industry. Genome sequences are now available for strains of many pathogenic and spoilage bacterial species commonly found in food, including dairy products. This information can be harnessed in the dairy production chain to improve molecular diagnostic methods that are either currently applied (e.g., flow cytometry) or under development (e.g., certain polymerase chain reaction (PCR) applications). Genomics approaches can be implemented for microbial enumeration and identification, control of bacterial growth, and the monitoring of antibiotic-resistant strains. This review examines the current status of genomics methods available to detect, quantify, and examine the activities of pathogens and spoilage bacteria present in dairy environments and provides an outlook for future applications of microbial genomics in milk. Once these technologies are routinely applied in the dairy production chain, our understanding of pathogenic and spoilage bacteria and their effect on the milk environment can be expected to increase dramatically.