Beyond the Total Plate Count: Metagenomic Applications for Meat and Poultry Processors
Advances in next-generation sequencing have allowed for an understanding of the microbial inhabitants that make up the microbiome in ways that culture-based techniques are limited
Today's commercial meat or poultry processing plant is a complex network of equipment, automation, human interaction, and multiple processes/pathways. These components work together to efficiently fabricate a carcass into multiple primal, subprimal, and trim cuts to be used for further processing. Here, they can be either packaged raw or further processed into ready-to-eat (RTE) meat items. At its core, this workflow has been successful for thousands of years in being able to create a wide variety of individual cuts of meat and further processed meat items such as sausage, which was noted as far back as Homer's Odyssey, written approximately 10,000 years ago.
While the processes have changed and advanced technology has been incorporated, one constant throughout the evolution of the meat industry has been the contribution of a very biologically diverse microbiome. This microbiome may contain thousands of different species of bacteria, viruses, and fungi living together as a community and taking residence in the animal, processing environment, and meat surfaces. The presence of specific bacteria within the microbial community can have both positive and negative effects on the safety and wholesomeness of the meat produced. The shelf life of both fresh and processed meat items is heavily influenced by the proliferation of select bacterial species within the meat microbiome under environmental conditions, which can result in undesirable characteristics of the product and a less-than-favorable experience for the consumer. Additionally, a critical focus of the meat and poultry industry has been the elimination of specific foodborne pathogens within the microbiome of the animal, plant environment, and ultimately the meat that is purchased by the consumer.