The next-generation tools for risk assessment and precision food safety in the One Health continuum

Abstract Sequencing technologies and bioinformatics are transforming microbiology and their applications, including aspects of food quality and precision food safety and description of microbial communities in the One Health context. The use of these protocols includes, among others, a deep understanding of the genomes of microorganisms in pure culture using whole genome sequencing and importantly, metagenomics has allowed the extensive comprehension of the microbiota and microbiome of samples. Microbial communities from different sources (clinical samples, environment, food-producing animals) have increasingly been studied to describe the genetic diversity, functionality, and succession of food-borne pathogens and for studying functional microorganisms used for producing novel foods and also using fermentation. This study presents the methods used for the description of microbial communities in a model fermented food, including culturing with a novel in situ culturing approach, full-length 16S rRNA gene sequencing, and shotgun metagenomic sequencing with computational enrichment. Several microorganisms were identified both in culture and as high-quality metagenome-assembled genomes and included prominent probiotic species of the genus Gluconobacter, Liquorilactobacillus, Lactiplantibacillus, Lentilactobacillus and Lacticaseibacillus that have potential health benefits and applications in food production and environment health enhancement. These tools can revolutionise risk assessment approaches, allowing for the pinpointing of contamination events, pathogens, antimicrobial resistance spread, and description of unknown beneficial microorganisms, as in this model study. The integration of these methods in the One Health continuum will allow the precise connection of samples from clinical settings, animals, plants, and their shared environment, achieving a holistic approach to food safety and public health. Key messages • technologies are changing food safety by enabling comprehensive analysis of microbiome. This can aid in identifying contamination events, pathogens, and AMR spread, and promote One Health integration. • Use of sequencing in foods, enables the identification of novel microbial species, providing valuable insights into the functional microorganisms for production and their potential health benefits.