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Review
. 2025 Aug 20:13:1638957.
doi: 10.3389/fbioe.2025.1638957. eCollection 2025.

Next-generation sequencing applications in food science: fundamentals and recent advances

Joel Tigrero-Vaca  1 , Byron Díaz  1 , Ganyu Gu  2 , Juan Manuel Cevallos-Cevallos  1
Affiliations
Review

Next-generation sequencing applications in food science: fundamentals and recent advances

Joel Tigrero-Vaca et al. Front Bioeng Biotechnol. .

Abstract

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: fermentation; food authentication; food microbiome; food safety; next-generation sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Schematic representation of the NGS workflow in food science, illustrating key steps including sample preparation and storage, DNA/RNA extraction, library preparation, sequencing, and the use of bioinformatics tools for various types of analysis including metagenetics, metagenomics, metatranscriptomics and WGS. Created using BioRender: https://BioRender.com.
FIGURE 2
FIGURE 2
Overview NGS applications in food fermentation, including microbial community analysis, starter culture formulation, flavor development, and process optimization. Created using BioRender: https://BioRender.com.
FIGURE 3
FIGURE 3
Schematic representation of AI and ML applications enabled by NGS in food science, including pathogen prediction, AMR tracking, fermentation quality control, and food authentication using models like random forest and multi-omics integration. Created using BioRender: https://BioRender.com.
See this image and copyright information in PMC

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