The old school way, and in many cases still in force, to study and detect food pathogen microorganisms meant obtaining samples, which we would plate on Petri dishes, see if anything grows, isolate the culture and identify the microorganism with a series of tests. However, the majority of the bacterial species cannot be cultured using this traditional way and, apart from that, they are time- and labor-consuming. Following latest trends in environmental microbiology, food microbiology has benefited from advances in molecular microbiology. Metagenomics is the application of modern genomic techniques in the study of the communities of microorganisms by direct sequencing their genome in the sample, bypassing the need for isolation and cultivation of individual species. These methods gradually became more common in food microbiology laboratories and this could pave the way for the universal application of metagenomics in the food safety field. Yet, they come with certain limitations that need to be addressed, in order to fully replace the traditional methods. In the present dissertation, we aimed to undertake a comparison between these techniques and discuss the possibility for this replacement to take place in the future.
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