Bioinformatic pipeline for profiling foodborne bacterial ecology and resistome from short-read metagenomics
Résumé
Next generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.
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