REVIEW article
Front. Bioeng. Biotechnol.
Sec. Industrial Biotechnology
Volume 13 - 2025 | doi: 10.3389/fbioe.2025.1638957
This article is part of the Research TopicTrigger the Microbiome Changes in Foods via Metagenomic Technologies: From Diagnostic to Potential Changes in Product Safety or Quality Risk ProfilesView all articles
Next-generation sequencing application in food science: Fundamentals and recent advances
Provisionally accepted
- 1Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politecnica del Litoral - Campus Prosperina, Guayaquil, Ecuador
- 2Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, Maryland, United States
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Next-generation sequencing (NGS) has revolutionized food science, offering unprecedented insights into microbial communities, food safety, fermentation, and product authenticity. NGS techniques, including metagenetics, metagenomics, and metatranscriptomics, enable culture-independent pathogen detection, antimicrobial resistance surveillance, and detailed microbial profiling, significantly improving food safety monitoring and outbreak prevention. In food fermentation, NGS has enhanced our understanding of microbial interactions, flavor formation, and metabolic pathways, contributing to optimized starter cultures and improved product quality. Furthermore, NGS has become a valuable tool in food authentication and traceability, ensuring product integrity and detecting fraud. Despite its advantages, challenges such as high sequencing costs, data interpretation complexity, and the need for standardized workflows remain. Future research focusing on optimizing real-time sequencing technologies, expanding multi-omics approaches, and addressing regulatory frameworks is suggested to fully harness NGS's potential in ensuring food safety, quality, and innovation.
Keywords: Next generation sequencing 1, food microbiome 2, fermentation 3, Food safety 4, food authentication 5
Received: 31 May 2025; Accepted: 05 Aug 2025.
Copyright: © 2025 Tigrero, Díaz, Gu and Cevallos-Cevallos. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Juan Manuel Cevallos-Cevallos, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Escuela Superior Politecnica del Litoral - Campus Prosperina, Guayaquil, Ecuador
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