Metagenomics of meat and poultry

This chapter focuses on the understanding and application of metagenomics as it applies to meat and poultry research. Key concepts for understanding metagenomics include how to conduct a metagenomic study from experimental design to analysis, the difference between shotgun metagenomics and 16S rRNA amplicon studies, and data visualization. Special consideration is also given to discussions on rarefaction and normalizing data. Application of metagenomics in meat and poultry production from both a food safety and a food quality standpoint is discussed in relation to the current body of work published and possible future directions. Meat and poultry food safety is framed around reduction and detection of pathogens, while food quality includes shelf life and packaging differences. The conditions in which animals are reared and the processing environments they are harvested in are considered in the context of impact on end food quality and safety. Additionally, the public heath and regulatory implications of using shotgun metagenomics as a tool for pathogen detection and reduction are addressed.