Trends in Microbiome and Digital One Health

The resident microbiota in food-processing plants can be the source of spoiling or pathogenic bacteria, that can proliferate during storage to unacceptable levels, compromising food quality and safety. Metagenomics-based monitoring of spoilage microorganisms in food-processing environment and mapping of the possible contamination routes is useful to prevent microbial spread along the processing chain and consequently the transition to the final product. Nevertheless, depending on the type of manufacturing considered, food processing microbiota may sometimes play a positive role. Indeed, cheese manufacturing plants often harbour lactic acid bacteria, beneficially involved in the fermentative and ripening processes. The use of metagenomics, although still limited in food industry, may be useful to understand the genomic mechanisms leading to spoilage or to the production of positive features during food production. In a next future, food processing industry will surely benefit of the integration of sequencing-based technologies for management and improvement of food quality and safety.