Advances in Food Metabolomics

1. Introduction

Food metabolomics is a rapidly evolving discipline that is transforming how we understand, monitor, and ensure the quality, safety, and traceability of food products. With its roots in systems biology, metabolomics focuses on the comprehensive analysis of small-molecule metabolites—compounds that represent the final downstream products of cellular activity. Since its formal emergence in 1999, metabolomics has become a vital tool for characterizing complex biological systems, and its application within food science has grown exponentially over the past two decades.

In the field of food science, metabolomics provides an unparalleled approach to unravel the intricate biochemical composition of agricultural products and processed foods. Unlike traditional analytical methods, which often target a limited set of known compounds, food metabolomics enables high-throughput, untargeted screening of hundreds to thousands of metabolites in a single run [1]. This capability is essential when analyzing food matrices, which are inherently diverse in composition and influenced by myriad factors such as species, geographic origin, agricultural practices, post-harvest treatments, storage conditions, and processing methods. These variables collectively define the metabolomic signature of a food product. Consequently, metabolomics facilitates the identification of chemical fingerprints and biomarkers that reflect nutritional quality, freshness, spoilage, contamination, and fraudulent practices [2].

Technological advancements have played a pivotal role in enhancing the capabilities of food metabolomics. Analytical platforms such as ultra-high-performance liquid chromatography (UHPLC), capillary electrophoresis (CE), nuclear magnetic resonance (NMR), and mass spectrometry (MS)—especially when combined with ionization methods such as electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI)—have improved the sensitivity, resolution, and reproducibility of metabolomic analysis [3]. For instance, UHPLC–QTOF and Orbitrap MS systems can now track changes in metabolites during thermal processing, fermentation, and storage, providing deeper insights into food quality and safety [4]. These systems also enable the identification and quantification of individual compounds in plant tissues, thus improving the understanding of their role in plant defense [5].

Rather than being used in isolation, food metabolomics is increasingly being complemented by multi-omics approaches. Integration with transcriptomics, proteomics, and lipidomics—collectively referred to as foodomics—enables a holistic assessment of molecular interactions within food systems [1]. This synergy is crucial for lipid profiling, flavor compound discovery, and the elucidation of metabolic responses during fermentation or processing. Multi-omics strategies also facilitate the detection of food fraud and enhance traceability. For example, untargeted LC-MS metabolomics has been used to discriminate geographical origin in nuts and coffee, while metabolomics combined with chemometrics aids in detecting adulteration in spices [2]. The field of food metabolomics is seeing continuous development in the range of analytical techniques that are now available to support its diverse range of applications [6].

Handling complex datasets remains a major challenge, prompting the development of robust chemometric and machine learning solutions. These approaches range from unsupervised methods such as principal component analysis (PCA) and hierarchical clustering to supervised methods such as orthogonal partial least squares (OPLSs), as well as emerging artificial neural networks (ANNs). They are now integral to metabolomic data interpretation and biomarker discovery [3]. The creation of shared metabolite databases and spectral libraries, along with retention-time alignment tools, has further improved compound identification and cross-study comparability [1].

In summary, food metabolomics is at the forefront of scientific innovation, offering unprecedented insights into the biochemical basis of food systems. Thanks to advancements in analytical platforms, data science methodologies, and integrated omics, the field is poised to drive new frontiers in food quality assurance, safety regulation, authenticity verification, and personalized nutrition.

2. An Overview of Published Articles

This Special Issue, “Advances in Food Metabolomics”, comprises six high-quality contributions, including five original research articles and one comprehensive review. These papers reflect the latest innovations and applications of metabolomics in food science. Together, these articles demonstrate the strength of metabolomics as a tool for profiling bioactive compounds, ensuring food safety, improving traceability, and providing nutritional and therapeutic insights.

In one of the featured studies, Colquhoun et al. [7] investigated the combined effect of thermogenic supplementation and resistance training in males. The authors highlighted how targeted nutritional strategies can modulate metabolic pathways to enhance fat loss without compromising performance. Yu et al. [8] presented a metabolomic and transcriptomic analysis of six distinct tissues of the lotus plant (Nelumbo nucifera), revealing tissue-specific flavonoid biosynthesis mechanisms with implications for quality control and functional food development.

Sánchez et al. [9] examined the clinical relevance of polyamine intake in ICU patients through an analysis of enteral nutrition formulas. Their findings underscore the need for optimized formulations to improve feeding tolerance and support recovery. Takács et al. [10] explored the stability and functionality of α-amylase inhibitors in common bean (Phaseolus vulgaris) under digestive conditions, offering insights into their nutraceutical potential for carbohydrate metabolism and weight management.

Song and Gong [11] utilized untargeted metabolomics to differentiate the metabolic signatures of Fructus Chebulae and Fructus Terminaliae Billericae, revealing significant variations in polyphenols, flavonoids, and terpenoids that could influence their traditional medicinal applications. Finally, the review by Sidira et al. [12] provided a comprehensive overview of how integrated omics—metabolomics, proteomics, and lipidomics—can be applied in seafood quality control and aquaculture. This article emphasizes the importance of multi-omics approaches in ensuring food safety, species identification, and disease management in aquatic systems.

3. Conclusions

Overall, the studies published in this Special Issue showcase the versatility of metabolomics in addressing both emerging and longstanding challenges in food science. These contributions range from profiling complex herbal matrices to assessing metabolite stability and functionality in clinical nutrition and aquaculture and highlight the expanding frontier of food metabolomics. They also demonstrate how metabolomics can be integrated with transcriptomics, proteomics, and traditional analytical methods to deliver deeper biological insights and practical outcomes for the food industry.

We would like to thank all the authors for their valuable contributions and all the reviewers for giving up their time and sharing their expertise to ensure the scientific rigor of this Special Issue. Our sincere thanks also go to the Applied Sciences editorial team for their support throughout the publication process. We hope that this Special Issue will serve as a valuable reference for researchers, technologists, and professionals working at the intersection of metabolomics and food science.