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Mechanistic Systems Biology of High-Salinity Fermented Seafood: Multi-Omics Integration for Microbial Safety and Quality Prediction
by
, , ,
Mia Yang Ang
1,2,3,*,†
,
Chen Li
3,4,†,
Heru Pramono
5,
Teck Yew Low
1,2,
Nur Azalina Suzianti Feisal
6,7,
Guat Jah Wong
3,4 and
Siew Woh Choo
3,4,8,9,* 1
Department of Biomedical Sciences, Jeffrey Cheah Sunway Medical School, Faculty of Medical and Life Sciences, Sunway University, Sunway City, Petaling Jaya 47500, Selangor, Malaysia
2
Sunway Microbiome Centre, Faculty of Medical and Life Sciences, Sunway University, Sunway City, Petaling Jaya 47500, Selangor, Malaysia
3
Zhejiang-Malaysia Joint Laboratory for Rare Medicinal Resources, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, China
4
College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, China
5
Department of Marine, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya 60115, East Java, Indonesia
6
MSU Centre for Climate Resilience and Strategy (m-CREST), Management and Science University, University Drive, Off Persiaran Olahraga, Shah Alam 40100, Selangor, Malaysia
7
Department of Diagnostics and Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, University Drive, Off Persiaran Olahraga, Shah Alam 40100, Selangor, Malaysia
8
International Frontier Interdisciplinary Research Institute (IFIRI), Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, China
9
Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ 07083, USA
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Biology 2026, 15(10), 772; https://doi.org/10.3390/biology15100772 (registering DOI)
Submission received: 28 April 2026
/
Revised: 7 May 2026
/
Accepted: 11 May 2026
/
Published: 12 May 2026
(This article belongs to the Section Microbiology)
Simple Summary
Traditional fermented and salted seafood products are important cultural and dietary foods, particularly in Asia. Their safety and quality depend on complex microbial communities that survive under strong environmental pressures, including high salt concentration, low water availability, pH changes, oxygen variation, and long fermentation periods. Earlier studies often focused on identifying which microorganisms are present, especially lactic acid bacteria. However, microbial presence alone does not explain how these organisms adapt, interact, produce desirable flavor compounds, or generate safety-related hazards such as biogenic amines. This review discusses how multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, can be integrated to understand microbial function in high-salinity fermented seafood. Rather than focusing mainly on databases and analytical tools, the review emphasizes the biological mechanisms linking microbial communities, environmental selection, enzyme activity, metabolite formation, and food safety outcomes. A conceptual framework based on histamine formation in Tetragenococcus halophilus is used to show how gene presence, gene expression, enzyme activity, and metabolite accumulation can be connected into a predictive safety model. This systems-level perspective can support earlier risk detection, improved process control, and more consistent production of safe, high-quality traditional fermented seafood.
Abstract
Foodborne diseases present a serious public health challenge, causing roughly 600 million illnesses and 420,000 deaths annually. A significant portion of this impact is felt in Asia, where traditional fermented and dry-salted seafood, such as katsuobushi, budu, and peda, are dietary staples. These products rely on diverse microbial communities that determine their final safety, flavor, texture, and shelf life. Historically, research has centered on lactic acid bacteria (LAB), yet the functional contributions of non-LAB halotolerant species, including genera like Tetragenococcus, Staphylococcus, and Bacillus, are functionally important in these high-salinity niches. This review evaluates the transition from basic taxonomic surveys to mechanistic multi-omics approaches, integrating genomics, transcriptomics, proteomics, and metabolomics to decode microbial functionality under selective environmental pressures. We discuss how genomic mining using platforms such as BAGEL4 and antiSMASH can uncover biosynthetic gene clusters and antimicrobial peptides, while CARD supports antimicrobial resistance monitoring. Transcriptomic analysis reveals microbial responses to osmotic stress, low water activity, and pH fluctuations, whereas proteomic profiling links gene expression to active enzymes, stress proteins, and functional biomarkers. Metabolomics captures the chemical outcomes of fermentation, including amino acids, volatile organic compounds, spoilage markers, and biogenic amines. By merging these high-dimensional datasets with artificial intelligence, researchers can move toward predictive modeling that distinguishes biological causation from simple correlation. This shift offers a strategy to improve the safety, consistency, and resilience of traditional high-salinity fermented seafood systems.
