Foodomics for investigations of food toxins

•Food contamination coming from bacterial toxins, mycotoxins and toxins from eukaryotic algae.•Poisoning by toxins coming from contaminated food.•Use of foodomics methods for identification and quantification of food borne pathogens and food toxins.

New nutritional trends and globalization of food market are substantially increasing food-borne outbreaks that remain a world-wide problem. Indeed, changes in consumers’ behavior, available production methods, food processing approaches, climate changes and microbial resistance bring some weak points within the food production and distribution lines where foodomics methods and novel protocols have been increasingly used to ensure food safety within the whole food production and distribution line. In this paper, foodomics technologies are described for precise identification of food pathogens and their toxins even on the strain/subtype level. In the near future further improvements in the methodologies and protocols should be mainly directed to generation of new databases, better throughput and standardization while increased food monitoring within the food production and distribution lines will be growingly demanded.