Shotgun metagenomics reveals differences in resistomes among probiotics, starter cultures, and cheeses. Resistomes of cheese, probiotics and starter cultures

Antibiotic resistance, which has been recognised as an urgent global problem, is evident throughout the entire agro-food chain. The findings on resistome in food microbiota, which serve as a potential carrier for transfer of antibiotic resistance genes (ARGs) to pathogenic bacteria, raise concerns for public health and food safety. From a One Health perspective, the human, animal, and environmental resistomes have been extensively studied, while the resistomes of different food systems remain largely unexplored. To address this knowledge gap, our study aims to improve the understanding of microbiomes and resistomes of food samples by using the advanced shotgun metagenomic sequencing technology. We focused on commercial products containing live lactic acid bacteria and bifidobacteria that are intentionally introduced into the agro-food chain (starter cultures and probiotic products) and a widely consumed group of fermented foods - cheeses. Understanding the composition of the microbiota and its resistome is not only crucial for the safety of these foods, but also offers significant opportunities to optimise the production of cheese and industrial cultures such as probiotics and starter cultures, ultimately helping us to address the global problem of antimicrobial resistance from a One-Health perspective.