There are a number of technologies and business applications that identify nucleic acids of various microorganisms. Technologies based on DNA analysis are the most promising direction in the molecular-genetic identification of the microbiota in food substrates. The present paper is a review of various aspects of microorganism identification in food substrates, their advantages and disadvantages. It features modern regulatory, scientific, and methodological sources, as well as patented solutions. The authors pay considerable attention to the classical methods and describe the use of polymerase chain reaction (PCR) in microbiota analysis. Then, they trace the development of next-generation sequencing (NGS) of DNA and how it can be used to identify pathogens in food substrates. So far, NGS proves to be the most advantageous method that identifies prokaryotic and eukaryotic microorganisms, as well as pathogens.
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