Towards a Universal Molecular Approach for the Quality Control of New Foodstuffs

Food safety and quality depend on raw material characteristics and on the chemical, physical and biotechnological processes adopted during food transformation. Microorganisms have been used in food production for thousands of years; bread is composed of both flour and yeast and a bottle of wine contains grape juice and several bacteria and yeasts. Today, microorganisms are also introduced in different food matrices (e.g. probiotics) to obtain so-called ‘functional foods’ which have beneficial effects on human health. In a traceability framework, foodstuffs can be treated as complex ecosystems where any biological component should be identified. In this chapter, a DNA barcoding approach is proposed as a universal, rapid and economical tool to characterize the whole biodiversity of a food ecosystem. Species or microbial strain identification relies on a comparison with DNA barcoding data from reference databases. Moreover, the species composition of complex food matrices and related pools of microorganisms (including pathogens) can be described by combining DNA barcoding identification with the newest high-throughput sequencing technologies.