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Metabolomic Technology in Quality and Safety of Agricultural Products and...
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Metabolomic Technology in Quality and Safety of Agricultural Products and Foods

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 9192

Special Issue Editor

Dr. Yasuhiro Date

E-Mail Website
Guest Editor
Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8642, Japan
Interests: metabolomics; NMR; data science; food chemistry; analytical chemistry; bioinformatics

Special Issue Information

Dear Colleagues,

Metabolomics is a powerful tool for the analysis and evaluation of the complex and diverse metabolite mixtures found in agricultural products and foods. Metabolomic studies provide useful information, e.g., how to improve nutritional and functional qualities, prevent food poisoning, and understand the processing and storage effects. In addition, the metabolomic technology in this field is constantly being advanced owing to the recent developments in computer science and information technology.

This Special Issue focuses on the recent advancements in metabolomic technology that has been made to address agricultural products and foods. The topics to be covered include an application of metabolomic technology for the evaluation and analysis of agricultural products and foods as well as the methodological advancements in metabolomic analysis using agricultural and food big data.

Dr. Yasuhiro Date
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolomics
  • metabolic profiling
  • metabolic fingerprinting
  • foodomics
  • nuclear magnetic resonance spectroscopy
  • mass spectrometry
  • multivariate analysis
  • machine learning

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Published Papers (7 papers)

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Research

23 pages, 1408 KiB  
Article
Storage Profiling: Evaluating the Effect of Modified Atmosphere Packaging on Metabolomic Changes of Strawberries (Fragaria × ananassa)
by Johannes Brockelt, Robin Dammann, Jennifer Griese, Agnes Weiss, Markus Fischer and Marina Creydt
Metabolites 2025, 15(5), 330; https://doi.org/10.3390/metabo15050330 - 15 May 2025
Abstract
Background/Objectives: Strawberries (Fragaria × ananassa) are among the most commonly consumed fruits due to their taste and nutritional benefits. However, their high rate of spoilage poses a major problem during the period from harvest and transport to further processing or marketing. [...] Read more.
Background/Objectives: Strawberries (Fragaria × ananassa) are among the most commonly consumed fruits due to their taste and nutritional benefits. However, their high rate of spoilage poses a major problem during the period from harvest and transport to further processing or marketing. The aim of this study was, therefore, to investigate the effects of passive modified atmosphere packaging on the metabolome and shelf life of strawberries as a more sustainable alternative compared to standard market storage conditions. Methods: A total of 99 strawberry samples were analyzed for microbial viable counts, water content, and metabolomic changes using non-targeted low-resolution near-infrared spectroscopy, high-resolution mass spectrometry, and microbial culture-based methods. Results: Using near-infrared spectroscopy as a rapid screening method, the linear regression model indicated that strawberries stored under modified atmosphere packaging conditions had a longer shelf life. Furthermore, lipidomic analysis using mass spectrometry showed that the levels of spoilage biomarkers, such as oxidized phosphatidylcholines and lysophosphatidylcholines, were increased under common market storage conditions without a controlled atmosphere. In contrast, the levels of these metabolites were reduced when strawberries were stored in modified atmosphere packaging. Moreover, the strawberries stored under modified atmosphere packaging had a lower number of bacteria, yeasts, and molds as well as a lower water loss throughout the entire storage period. Conclusions: Overall, the study highlights the potential of passive modified atmosphere packaging films to extend the shelf life and thus maintain the edibility of strawberries over a longer period. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
18 pages, 2892 KiB  
Article
Effects of Roasting Process on Sensory Qualities, Color, Physicochemical Components, and Identification of Key Aroma Compounds in Hubei Strip-Shaped Green Tea
by Fei Ye, Anhui Gui, Xiaoyan Qiao, Panpan Liu, Xueping Wang, Shengpeng Wang, Lin Feng, Jin Teng, Jinjin Xue, Xun Chen, Yuanhong Mei, Binghua Zhang, Hanshan Han, Anhua Liao, Pengcheng Zheng and Shiwei Gao
Metabolites 2025, 15(3), 155; https://doi.org/10.3390/metabo15030155 - 25 Feb 2025
Viewed by 484
Abstract
Background: Roasting conditions significantly influence the sensory profile of Hubei strip-shaped green tea (HSSGT). Methods: This study examined the effects of roast processing on the sensory attributes, color qualities, physicochemical properties, and key aroma compounds of HSSGT. Sensory evaluation, color qualities determination, principal [...] Read more.
Background: Roasting conditions significantly influence the sensory profile of Hubei strip-shaped green tea (HSSGT). Methods: This study examined the effects of roast processing on the sensory attributes, color qualities, physicochemical properties, and key aroma compounds of HSSGT. Sensory evaluation, color qualities determination, principal component analysis of physicochemical components (PCA), HS-SPME (headspace solid-phase microextraction) coupled with GC-MS (gas chromatography–mass spectrometry), relative odor activity value (ROAV), gas chromatography–olfactometry (GC-O), and absolute quantification analysis were employed to identify the critical difference in compounds that influence HSSGT desirability. Results: The results indicated that HSSGT roasted at 110 °C for 14 min achieved the highest sensory scores, superior physicochemical qualities, and an enhanced aroma index, which was attributed to shifting the proportion of chestnut to floral volatile compounds. Additionally, sensory-guided ROAV, GC-O, and absolute quantification revealed that linalool, octanal, nonanal, and hexanal were the most significant volatile compounds. The variations in these four critical compounds throughout the roasting process were further elucidated, showing that the ideal roasting conditions heightened floral aromas while diminishing the presence of less desirable green odors. These findings offer technical guidance and theoretical support for producing HSSGT with a more desirable balance of chestnut and floral aroma characteristics. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
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18 pages, 7282 KiB  
Article
Untargeted Metabolite Profiling Reveals Acute Toxicity of Pentosidine on Adipose Tissue of Rats
by Chuanqin Hu, Zhenzhen Shao, Wei Wu and Jing Wang
Metabolites 2024, 14(10), 539; https://doi.org/10.3390/metabo14100539 - 9 Oct 2024
Viewed by 1257
Abstract
Background: Pentosidine is an advanced glycation end product that is commonly found in heat-processed foods. Pentosidine has been involved in the occurrence and development of some chronic diseases. It was reported that pentosidine exposure can impair the function of the liver and [...] Read more.
Background: Pentosidine is an advanced glycation end product that is commonly found in heat-processed foods. Pentosidine has been involved in the occurrence and development of some chronic diseases. It was reported that pentosidine exposure can impair the function of the liver and kidneys. Adipose tissue, as an active endocrine organ, plays an important role in maintaining the normal physiological function of cells. However, the metabolic mechanism that causes pentosidine to induce toxicity in adipose tissue remains unclear. Methods: In the study, thirty male Sprague-Dawley rats were divided into a normal diet group, low dose group, and high dose group. A non-targeted metabolomics approach was used to compare the metabolic profiles of adipose tissue between the pentosidine and normal diet groups. Furthermore, histopathological observation and body weight change analysis were performed to test the results of the metabolomics analysis. Results: A total of forty-two differential metabolites were identified. Pentosidine mainly disturbed twelve metabolic pathways, such as ascorbate and aldarate metabolism, glycine, serine, and threonine metabolism, sulfur metabolism, pyruvate metabolism, etc. Additionally, pyruvic acid was identified as a possible key upregulated metabolite involved in thirty-four metabolic pathways. α-Ketoglutaric acid was named as a probable key downregulated metabolite involved in nineteen metabolic pathways based on enrichment network analysis. In addition, histopathological analysis and body weight changes confirmed the results of the metabolomics analysis. Conclusions: These results provided a new perspective for the molecular mechanisms of adipose tissue toxicity induced by pentosidine. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
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13 pages, 5376 KiB  
Article
An Exploratory Study on the Rapid Detection of Volatile Organic Compounds in Gardenia Fruit Using the Heracles NEO Ultra-Fast Gas Phase Electronic Nose
by Wenjing Cai, Wei Zhou, Jiayao Liu, Jing Wang, Ding Kuang, Jian Wang, Qing Long and Dan Huang
Metabolites 2024, 14(8), 445; https://doi.org/10.3390/metabo14080445 - 11 Aug 2024
Viewed by 1143
Abstract
Gardenia fruit is a popular functional food and raw material for natural pigments. It comes from a wide range of sources, and different products sharing the same name are very common. Volatile organic compounds (VOCs) are important factors that affect the flavor and [...] Read more.
Gardenia fruit is a popular functional food and raw material for natural pigments. It comes from a wide range of sources, and different products sharing the same name are very common. Volatile organic compounds (VOCs) are important factors that affect the flavor and quality of gardenia fruit. This study used the Heracles NEO ultra-fast gas phase electronic nose with advanced odor analysis performance and high sensitivity to analyze six batches of gardenia fruit from different sources. This study analyzed the VOCs to find a way to quickly identify gardenia fruit. The results show that this method can accurately distinguish the odor characteristics of various gardenia fruit samples. The VOCs in gardenia fruit are mainly organic acid esters, ketones, and aldehyde compounds. By combining principal component analysis (PCA) and discriminant factor analysis (DFA), this study found that the hexanal content varied the most in different gardenia fruit samples. The VOCs allowed for the fruit samples to be grouped into two main categories. One fruit sample was quite different from the fruits of other origins. The results provide theoretical support for feasibility of rapid identification and quality control of gardenia fruit and related products in the future. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
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23 pages, 5065 KiB  
Article
Adenosine Triphosphate and Adenylate Energy Charge in Ready-to-Eat Food
by Georgii Konoplev, Alar Sünter, Artur I. Kuznetsov, Piret Raudsepp, Tõnu Püssa, Lauri Toom, Linda Rusalepp, Dea Anton, Oksana V. Stepanova, Daniil Lyalin, Liubov Abramova, Andrey Kozin, Oksana S. Stepanova, Aleksandr Frorip and Mati Roasto
Metabolites 2024, 14(8), 440; https://doi.org/10.3390/metabo14080440 - 7 Aug 2024
Viewed by 1435
Abstract
It is commonly accepted that dietary nucleotides should be considered as essential nutrients originating mainly but not exclusively from meat and fish dishes. Most research in food science related to nutrition nucleotides is focused on raw products, while the effects of thermal processing [...] Read more.
It is commonly accepted that dietary nucleotides should be considered as essential nutrients originating mainly but not exclusively from meat and fish dishes. Most research in food science related to nutrition nucleotides is focused on raw products, while the effects of thermal processing of ready-to-eat food on nucleotide content are largely overlooked by the scientific community. The aim of this study is to investigate the impact of thermal processing and cold storage on the content of dietary nucleotides in freshly prepared and canned ready-to-eat meat and fish food. The concentrations of ATP, ADP, AMP, IMP, Ino, and Hx were determined using NMR, HPLC, FPMLC, and ATP bioluminescence analytical techniques; freshness indices K and K1 and adenylate energy charge (AEC) values were estimated to assess the freshness status and confirm a newly unveiled phenomenon of the reappearance of adenylate nucleotides. It was found that in freshly prepared at 65 °C ≤ T ≤ +100 °C and canned food, the concentration of free nucleotides was in the range of 0.001–0.01 µmol/mL and remained unchanged for a long time during cold storage; the correct distribution of mole fractions of adenylates corresponding to 0 < AEC < 0.5 was observed compared to 0.2 < AEC < 1.0 in the original raw samples, with either a high or low content of residual adenylates. It could be assumed that heating at nonenzymatic temperatures T > 65 °C can rupture cell membranes and release residual intracell nucleotides in quite a meaningful concentration. These findings may lead to a conceptual change in the views on food preparation processes, taking into account the phenomenon of the free adenylates renaissance and AEC bioenergetics. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
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13 pages, 13204 KiB  
Article
Explorative Study on Volatile Organic Compounds of Cinnamon Based on GC-IMS
by Yu Pan, Liya Qiao, Shanshuo Liu, Ye He, Danna Huang, Wuwei Wu, Yingying Liu, Lu Chen and Dan Huang
Metabolites 2024, 14(5), 274; https://doi.org/10.3390/metabo14050274 - 9 May 2024
Cited by 3 | Viewed by 1958
Abstract
Cinnamon is one of the most popular spices worldwide, and volatile organic compounds (VOCs) are its main metabolic products. The misuse or mixing of cinnamon on the market is quite serious. This study used gas chromatography-ion migration spectroscopy (GC-IMS) technology to analyze the [...] Read more.
Cinnamon is one of the most popular spices worldwide, and volatile organic compounds (VOCs) are its main metabolic products. The misuse or mixing of cinnamon on the market is quite serious. This study used gas chromatography-ion migration spectroscopy (GC-IMS) technology to analyze the VOCs of cinnamon samples. The measurement results showed that 66 VOCs were detected in cinnamon, with terpenes being the main component accounting for 45.45%, followed by aldehydes accounting for 21.21%. The content of esters and aldehydes was higher in RG-01, RG-02, and RG-04; the content of alcohols was higher in RG-01; and the content of ketones was higher in RG-02. Principal component analysis, cluster analysis, and partial least squares regression analysis can be performed on the obtained data to clearly distinguish cinnamon. According to the VIP results of PLS-DA, 1-Hexanol, 2-heptanone, ethanol, and other substances are the main volatile substances that distinguish cinnamon. This study combined GC-IMS technology with chemometrics to accurately identify cinnamon samples, providing scientific guidance for the efficient utilization of cinnamon. At the same time, this study is of great significance for improving the relevant quality standards of spices and guiding the safe use of spices. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
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17 pages, 2604 KiB  
Article
A Data-Driven Approach to Sugarcane Breeding Programs with Agronomic Characteristics and Amino Acid Constituent Profiling
by Chiaki Ishikawa, Yasuhiro Date, Makoto Umeda, Yusuke Tarumoto, Megumi Okubo, Yasujiro Morimitsu, Yasuaki Tamura, Yoichi Nishiba and Hiroshi Ono
Metabolites 2024, 14(4), 243; https://doi.org/10.3390/metabo14040243 - 21 Apr 2024
Cited by 1 | Viewed by 1864
Abstract
Sugarcane (Saccharum spp. hybrids) and its processed products have supported local industries such as those in the Nansei Islands, Japan. To improve the sugarcane quality and productivity, breeders select better clones by evaluating agronomic characteristics, such as commercially recoverable sugar and cane [...] Read more.
Sugarcane (Saccharum spp. hybrids) and its processed products have supported local industries such as those in the Nansei Islands, Japan. To improve the sugarcane quality and productivity, breeders select better clones by evaluating agronomic characteristics, such as commercially recoverable sugar and cane yield. However, other constituents in sugarcane remain largely unutilized in sugarcane breeding programs. This study aims to establish a data-driven approach to analyze agronomic characteristics from breeding programs. This approach also determines a correlation between agronomic characteristics and free amino acid composition to make breeding programs more efficient. Sugarcane was sampled in clones in the later stage of breeding selection and cultivars from experimental fields on Tanegashima Island. Principal component analysis and hierarchical cluster analysis using agronomic characteristics revealed the diversity and variability of each sample, and the data-driven approach classified cultivars and clones into three groups based on yield type. A comparison of free amino acid constituents between these groups revealed significant differences in amino acids such as asparagine and glutamine. This approach dealing with a large volume of data on agronomic characteristics will be useful for assessing the characteristics of potential clones under selection and accelerating breeding programs. Full article
(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)
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