About this Research Topic
With the ability to precisely identify entire microbial communities in a single food, ingredient, or environmental sample, genomic-based approaches like shotgun, long-read metagenomics, and metabarcoding represent the next disruptive revolution in food safety diagnostics. The detection and analysis of microbiological pathogens is being revolutionized by this technology, which also makes it possible to quickly identify and control foodborne outbreaks, improves public health outcomes, and lessens the need for costly recalls.
But as metagenomics becomes more widely used, it should improve our comprehension of the basic mechanisms underlying the emergence and spread of bacteria in the food chain. Instead of concentrating on limiting a single hazard without considering its complete effects and interrelationships throughout the entire food chain, this understanding should guide the creation of more focused and successful system-wide interventions.
From a regulatory standpoint, the likelihood of misclassification and the difficulty of determining a limit of detection, particularly of a pathogen at low levels in a sample limits the use of these technologies. The lower abundant pathogen species are excluded from the interpretation, thus standardized techniques that enable the precise detection and measurements are required.
The main goal of this Research Topic is to provide insights into metagenomic techniques for studying the microbiota associated with foods, in special raw materials such fruits and vegetable for both diagnostic and risk assessment measurements.
Authors are encouraged to submit research articles and/or review articles on the following topics:
• Metagenomic technologies as food safety diagnostics.
• Tracking pathogens during plant growth and final product.
• Detection of antibiotic and metal resistant genes.
• Knowledge gaps, limitations, and opportunities for food safety.
• Identification of uncultivable emerging pathogens and re-think the safety risk assessment measurements.
• Application of metagenomics technologies.
But as metagenomics becomes more widely used, it should improve our comprehension of the basic mechanisms underlying the emergence and spread of bacteria in the food chain. Instead of concentrating on limiting a single hazard without considering its complete effects and interrelationships throughout the entire food chain, this understanding should guide the creation of more focused and successful system-wide interventions.
From a regulatory standpoint, the likelihood of misclassification and the difficulty of determining a limit of detection, particularly of a pathogen at low levels in a sample limits the use of these technologies. The lower abundant pathogen species are excluded from the interpretation, thus standardized techniques that enable the precise detection and measurements are required.
The main goal of this Research Topic is to provide insights into metagenomic techniques for studying the microbiota associated with foods, in special raw materials such fruits and vegetable for both diagnostic and risk assessment measurements.
Authors are encouraged to submit research articles and/or review articles on the following topics:
• Metagenomic technologies as food safety diagnostics.
• Tracking pathogens during plant growth and final product.
• Detection of antibiotic and metal resistant genes.
• Knowledge gaps, limitations, and opportunities for food safety.
• Identification of uncultivable emerging pathogens and re-think the safety risk assessment measurements.
• Application of metagenomics technologies.
Keywords: Metabarcoding, Next-generation sequencing, Shotgun metagenomics, Long-read metagenomics, Food safety, Food quality, Antibiotic resistant genes (ARG), Metal resistant genes (MRG), Fruits, Vegetables
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
