Advances in Food Sciences: Metabolomics to Unravel the Complexity of Food Metabolites

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Food Metabolomics".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 13320

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Department of Metabolism, Digestion and Reproduction, Section of Nutrition, Faculty of Medicine, Commonwealth Building, Hammersmith Campus, Imperial College London, London W12 0NN, UK
Interests: metabolic phenotyping; inflammatory bowel disease; personalized nutrition; pharmacology; toxicology
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Special Issue Information

Dear Colleagues,

Nutritional dark matter relates to those unknown compounds that we eat daily, and food, a member of the exposome, has crucial health implications. It is well known that nutrition-fact labels inform mainly about calories, macronutrients (fat, protein, carbohydrates), and micronutrients (vitamins, minerals). And sometimes, the names of the ingredients used are also reported on the package of the food we eat. However, there is a big gap to fill in knowing at a molecular level all the compounds we eat as what is reported is not sufficient, because food is more complex in its chemistry and biology. For instance, carbohydrates represent a big challenge to study per se. The challenge continues for those compounds that are not characterized yet and that in turn precludes their study on their possible effects on health to know which ones could be beneficial, inert, or detrimental, and whether they act on their own or in combination with other compounds to produce a biological activity.

It gets more complicated when food is cooked as the way it is cooked could produce chemical reactions that transform “raw” compounds into different ones. This gets even more complex due to inter-individual differences in response to the same compound. Furthermore, these unknown compounds could be at very low concentrations, which could imply no effect. However, it is known that some compounds (like some drugs or vitamins) can exert biological activity at low concentrations (i.e., dose), effect known as hormesis.

The chemistry of food components is complex, and complex is the effects they may have on both sides of the superorganism, the host, and its microbiome. The classical instance for this is choline contained in eggs, poultry, dairy, red meat, and seafood, whereby TMAO is produced through combinatorial metabolism between the host and its microbiota, and it has cardiovascular implications such as atherosclerosis. Therefore, knowing the dark matter in our diet and its effects on our health, dietary recommendation can be improved towards personalised nutrition.

Ergo, this Special Issue welcomes clinical and non-clinical studies using metabolomics approach to unveil new compounds from food, and if possible, their biological effects. Hyphenated mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) are the analytical platforms to be considered. Regarding MS, this Special Issue will focus on chromatography (e.g., gas chromatography (GC), liquid chromatography (LC), or ion chromatography (IC)) or capillary electrophoresis (CE) hyphenated with MS.

Systematic reviews and meta-analyses on this topic are also welcome. 

Dr. José Iván Serrano-Contreras
Guest Editor

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Keywords

  • foodomics
  • nutrimetabolomics
  • phytochemicals
  • food chemistry
  • food analysis
  • dark matter in diet
  • nutritional dark matter
  • nutritional hormesis
  • untargeted/targeted analysis

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Published Papers (3 papers)

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Research

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14 pages, 5912 KB  
Article
Effects of Macrococcus caseolyticus on the Volatile Flavor Substances of Chinese-Style Sausage
by Yuanqing Gu, Xinya Chen, Jingjing Mao, Xin Nie, Chenglin Zhu, Qin Zou, Qiqi Luo, Yudi Zeng, Luca Laghi, Gianfranco Picone and Zhiping Zhao
Metabolites 2025, 15(9), 570; https://doi.org/10.3390/metabo15090570 - 26 Aug 2025
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Abstract
Objectives: The primary objective of this study was to investigate the effects of Macrococcus caseolyticus isolated from Chinese bacon on the quality of Chinese-style sausages. Methods: The physicochemical properties and volatile flavor compounds (VOCs) of sausages inoculated with M. caseolyticus at different concentrations [...] Read more.
Objectives: The primary objective of this study was to investigate the effects of Macrococcus caseolyticus isolated from Chinese bacon on the quality of Chinese-style sausages. Methods: The physicochemical properties and volatile flavor compounds (VOCs) of sausages inoculated with M. caseolyticus at different concentrations (105, 106, and 107 CFU/g) were investigated. VOCs were detected using gas chromatography–ion mobility spectrometry (GC-IMS). Results: The sausages inoculated with M. caseolyticus showed progressive decreases in Aw, total volatile base nitrogen (TVB-N), malondialdehyde and carbonyl content during fermentation compared to the control sausage. A total of 90 VOCs were identified based on GC-IMS analysis, including 20 esters, 17 aldehydes, 22 alcohols, 12 ketones, 5 acids compounds, and 14 other compounds. M. caseolyticus-inoculated sausages exhibited elevated levels in alcohols and aldehydes, while the content of ketones was reduced compared to the control sausage. Multivariate statistical analysis indicated the significant differences in volatile flavor profiles among the sample and control sausages. Notably, seven VOCs in sausages, including 1-octen-3-ol, isoamyl alcohol, heptanal, hexanal, methyl 2-methylbutyrate, ethyl isovalerate and 2-pinene, were identified as the key aroma compounds (ROAV ≥ 1). Conclusions: The fermented sausages inoculated with different concentrations of M. caseolyticus exhibited significant differences in VOCs. This study provides the support for employing M. caseolyticus to improve the overall quality and flavor profile of Chinese-style sausage. Full article
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18 pages, 1585 KB  
Article
Modeling the Sensory Characteristics of Japanese Sake Using the Sake Metabolome Analysis Method
by Takuji Kobayashi, Yuko Komatsu-Hata, Ryota Saito, Hisashi Yazawa, Masayuki Takahashi, Ken Oda and Kazuhiro Iwashita
Metabolites 2025, 15(8), 559; https://doi.org/10.3390/metabo15080559 - 20 Aug 2025
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Abstract
Background/Objectives: The components of food and beverages are important elements that determine their palatability. Although the components of sake, a traditional Japanese alcoholic beverage, have been studied for many years, their correlation with sensory characteristics is unclear. Methods: We investigate the correlation with [...] Read more.
Background/Objectives: The components of food and beverages are important elements that determine their palatability. Although the components of sake, a traditional Japanese alcoholic beverage, have been studied for many years, their correlation with sensory characteristics is unclear. Methods: We investigate the correlation with the sake metabolome analysis method developed by our group using ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry. We constructed orthogonal projections to latent structure models to predict sensory evaluation data obtained through the quantitative descriptive analysis method from the sake metabolome data. Results: For two years of study, 8 sensory evaluation models of the 2016 brewing year and 11 sensory evaluation models of the 2017 brewing year, including color, ethyl hexanoate, Hine-ka, Nama hine-ka, ethyl acetate, grainy/sweet aroma, sweetness, sourness, body, astringency, harsh taste/acrid taste, aftertaste, and overall quality, demonstrated a predictive performance with Q2 > 0.5. Liquid chromatography-based analytical data indicated that it is possible to predict not only taste but also aroma. Additionally, the generalization performance of the prediction models for sensory evaluation attributes common to both years was verified. Conclusions: These results provide a new option for explaining the sensory characteristics of sake from its components and contribute to a deeper understanding of them. Full article
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Review

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31 pages, 1017 KB  
Review
Nutritional Modulation of the Gut–Brain Axis: A Comprehensive Review of Dietary Interventions in Depression and Anxiety Management
by Mariana Merino del Portillo, Vicente Javier Clemente-Suárez, Pablo Ruisoto, Manuel Jimenez, Domingo Jesús Ramos-Campo, Ana Isabel Beltran-Velasco, Ismael Martínez-Guardado, Alejandro Rubio-Zarapuz, Eduardo Navarro-Jiménez and José Francisco Tornero-Aguilera
Metabolites 2024, 14(10), 549; https://doi.org/10.3390/metabo14100549 - 14 Oct 2024
Cited by 13 | Viewed by 11183
Abstract
Mental health is an increasing topic of focus since more than 500 million people in the world suffer from depression and anxiety. In this multifactorial disorder, parameters such as inflammation, the state of the microbiota and, therefore, the patient’s nutrition are receiving more [...] Read more.
Mental health is an increasing topic of focus since more than 500 million people in the world suffer from depression and anxiety. In this multifactorial disorder, parameters such as inflammation, the state of the microbiota and, therefore, the patient’s nutrition are receiving more attention. In addition, food products are the source of many essential ingredients involved in the regulation of mental processes, including amino acids, neurotransmitters, vitamins, and others. For this reason, this narrative review was carried out with the aim of analyzing the role of nutrition in depression and anxiety disorders. To reach the review aim, a critical review was conducted utilizing both primary sources, such as scientific publications and secondary sources, such as bibliographic indexes, web pages, and databases. The search was conducted in PsychINFO, MedLine (Pubmed), Cochrane (Wiley), Embase, and CinAhl. The results show a direct relationship between what we eat and the state of our nervous system. The gut–brain axis is a complex system in which the intestinal microbiota communicates directly with our nervous system and provides it with neurotransmitters for its proper functioning. An imbalance in our microbiota due to poor nutrition will cause an inflammatory response that, if sustained over time and together with other factors, can lead to disorders such as anxiety and depression. Changes in the functions of the microbiota–gut–brain axis have been linked to several mental disorders. It is believed that the modulation of the microbiome composition may be an effective strategy for a new treatment of these disorders. Modifications in nutritional behaviors and the use of ergogenic components are presented as important non-pharmacological interventions in anxiety and depression prevention and treatment. It is desirable that the choice of nutritional and probiotic treatment in individual patients be based on the results of appropriate biochemical and microbiological tests. Full article
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