Research Topic

Genomics and metagenomics approaches for food value chain quality, safety, and product development

About this Research Topic

Genomics and metagenomics techniques have revolutionized investigations of microbial activity along the complete food value chain, from farm to fork, advancing insight into functional roles of microbial strains and consortia in food quality and safety. Advances in 2nd- and 3rd-generation DNA sequencing technologies and computational methods for microbial data science have paved the way for multi-omics characterization of microbial communities in agriculture and food production, with myriad applications including pathogen tracing, functional characterization, and microbial ecology. Genomics applied to food production could be a new trend for routine food chain management, but critical assessment and future direction are needed, including better standardization, interoperability, and quality control in food applications.

Food safety and quality management regimes typically employ traditional methods for microbial detection and characterization, which have known limitations including levels of detection and resolution. Genomics and metagenomics methods have numerous benefits that overcome these limitations, offering potential applications that could improve food safety, quality, and sustainability. Nevertheless, other limitations must be addressed, including standardization and best practices for food applications.

The goal of this Research Topic is to critically evaluate applications of new nucleotide sequencing technologies and analysis techniques in food quality and safety throughout the food value chain. This encompasses genomics and metagenomics applications that span raw materials production to final products. Efforts to make genomics and metagenomics technologies accessible and standardized are welcome if they demonstrate added value in farm-to-fork.

Suitable topics include any applications of 2nd- and 3rd-generation sequencing technologies for genomics and metagenomics in food microbiology, e.g., genomics of foodborne pathogens or beneficial food microbes, bioinformatics techniques and digital resources with specific applications in food quality and safety, foods as model systems for microbial ecology, and genomics and metagenomics applications in food fermentation. The focus is on Original Research articles, but other article types (Original Research, Review, Mini-Review, Method, Perspective, Hypothesis and Theory, and Opinion) will be considered.

Caroline Barretto is currently Senior Bioinformatics Specialist at Nestlé Institute of Food Safety and Analytical Sciences


Keywords: Genomics, metagenomics, microbiome, food quality, food safety, food processing, fermentation, agriculture, microbial ecology, soil ecology, green label, shelf-life monitoring, spoilage management, phages, bacteriophages, culturomics


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.

Genomics and metagenomics techniques have revolutionized investigations of microbial activity along the complete food value chain, from farm to fork, advancing insight into functional roles of microbial strains and consortia in food quality and safety. Advances in 2nd- and 3rd-generation DNA sequencing technologies and computational methods for microbial data science have paved the way for multi-omics characterization of microbial communities in agriculture and food production, with myriad applications including pathogen tracing, functional characterization, and microbial ecology. Genomics applied to food production could be a new trend for routine food chain management, but critical assessment and future direction are needed, including better standardization, interoperability, and quality control in food applications.

Food safety and quality management regimes typically employ traditional methods for microbial detection and characterization, which have known limitations including levels of detection and resolution. Genomics and metagenomics methods have numerous benefits that overcome these limitations, offering potential applications that could improve food safety, quality, and sustainability. Nevertheless, other limitations must be addressed, including standardization and best practices for food applications.

The goal of this Research Topic is to critically evaluate applications of new nucleotide sequencing technologies and analysis techniques in food quality and safety throughout the food value chain. This encompasses genomics and metagenomics applications that span raw materials production to final products. Efforts to make genomics and metagenomics technologies accessible and standardized are welcome if they demonstrate added value in farm-to-fork.

Suitable topics include any applications of 2nd- and 3rd-generation sequencing technologies for genomics and metagenomics in food microbiology, e.g., genomics of foodborne pathogens or beneficial food microbes, bioinformatics techniques and digital resources with specific applications in food quality and safety, foods as model systems for microbial ecology, and genomics and metagenomics applications in food fermentation. The focus is on Original Research articles, but other article types (Original Research, Review, Mini-Review, Method, Perspective, Hypothesis and Theory, and Opinion) will be considered.

Caroline Barretto is currently Senior Bioinformatics Specialist at Nestlé Institute of Food Safety and Analytical Sciences


Keywords: Genomics, metagenomics, microbiome, food quality, food safety, food processing, fermentation, agriculture, microbial ecology, soil ecology, green label, shelf-life monitoring, spoilage management, phages, bacteriophages, culturomics


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.

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Submission Deadlines

31 October 2021 Abstract
28 February 2022 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

31 October 2021 Abstract
28 February 2022 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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