CRISPR-Directed Microbiome Manipulation across the Food Supply Chain

The advent of CRISPR-based technologies has revolutionized genetics over the past decade, and genome editing is now widely implemented for diverse medical and agricultural applications, such as correcting genetic disorders and improving crop and livestock breeding. CRISPR-based technologies are also of great potential to alter the genetic content of food bacteria in order to control the composition and activity of microbial populations across the food supply chain, from the farm to consumer products. Advancing the food supply chain is of great societal importance as it involves optimizing fermentation processes to enhance taste and sensory properties of food products, as well as improving food quality and safety by controlling spoilage bacteria and pathogens. Here, we discuss the various CRISPR technologies that can alter bacterial functionalities and modulate the composition of microbial communities in foods. We illustrate how these applications can be harnessed along the food supply chain to manipulate microbiomes that encompass spoilage and pathogenic bacteria as well as desirable starter cultures and health-promoting probiotics.