Next-generation sequencing applications in food science: fundamentals and recent advances
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 detect...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Bioengineering and Biotechnology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbioe.2025.1638957/full |
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| author | Joel Tigrero-Vaca Byron Díaz Ganyu Gu Juan Manuel Cevallos-Cevallos |
| author_facet | Joel Tigrero-Vaca Byron Díaz Ganyu Gu Juan Manuel Cevallos-Cevallos |
| author_sort | Joel Tigrero-Vaca |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-09e997f66ceb48f5bca6b5bbe43e078e |
| institution | Kabale University |
| issn | 2296-4185 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioengineering and Biotechnology |
| spelling | doaj-art-09e997f66ceb48f5bca6b5bbe43e078e2025-08-20T05:32:45ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852025-08-011310.3389/fbioe.2025.16389571638957Next-generation sequencing applications in food science: fundamentals and recent advancesJoel Tigrero-Vaca0Byron Díaz1Ganyu Gu2Juan Manuel Cevallos-Cevallos3Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Guayaquil, EcuadorEscuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Guayaquil, EcuadorEnvironmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD, United StatesEscuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Guayaquil, EcuadorNext-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.https://www.frontiersin.org/articles/10.3389/fbioe.2025.1638957/fullnext-generation sequencingfood microbiomefermentationfood safetyfood authentication |
| spellingShingle | Joel Tigrero-Vaca Byron Díaz Ganyu Gu Juan Manuel Cevallos-Cevallos Next-generation sequencing applications in food science: fundamentals and recent advances Frontiers in Bioengineering and Biotechnology next-generation sequencing food microbiome fermentation food safety food authentication |
| title | Next-generation sequencing applications in food science: fundamentals and recent advances |
| title_full | Next-generation sequencing applications in food science: fundamentals and recent advances |
| title_fullStr | Next-generation sequencing applications in food science: fundamentals and recent advances |
| title_full_unstemmed | Next-generation sequencing applications in food science: fundamentals and recent advances |
| title_short | Next-generation sequencing applications in food science: fundamentals and recent advances |
| title_sort | next generation sequencing applications in food science fundamentals and recent advances |
| topic | next-generation sequencing food microbiome fermentation food safety food authentication |
| url | https://www.frontiersin.org/articles/10.3389/fbioe.2025.1638957/full |
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