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Journal = Foods
Section = Foodomics

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18 pages, 5124 KiB  
Article
Effects of Different Drying Methods on the Quality of Forest Ginseng Revealed Based on Metabolomics and Enzyme Activity
by Junjia Xing, Xue Li, Wenyu Dang, Limin Yang, Lianxue Zhang, Wei Li, Yan Zhao, Jiahong Han and Enbo Cai
Foods 2025, 14(15), 2753; https://doi.org/10.3390/foods14152753 - 7 Aug 2025
Abstract
Forest ginseng (FG) is a rare medicinal and culinary plant in China, and its drying quality is heavily dependent on the drying method. This study investigated the effects of traditional hot air drying (HAD) and the self-developed negative-pressure circulating airflow-assisted desiccator drying (PCAD) [...] Read more.
Forest ginseng (FG) is a rare medicinal and culinary plant in China, and its drying quality is heavily dependent on the drying method. This study investigated the effects of traditional hot air drying (HAD) and the self-developed negative-pressure circulating airflow-assisted desiccator drying (PCAD) method on the quality of FG using metabolomics and enzyme activity. The results revealed that the enzyme activities of dried FG were reduced considerably. PCAD preserved higher enzyme activity than HAD. Metabolomics data demonstrate that HAD promotes the formation of primary metabolites (amino acids, lipids, nucleotides, etc.), whereas PCAD promotes the formation of secondary metabolites (terpenoids, phenolic acids, etc.). A change-transformation network was built by combining the metabolites listed above and their biosynthetic pathways, and it was discovered that these biosynthetic pathways were primarily associated with the mevalonate (MVA) pathway, lipid metabolism, phenylpropane biosynthesis, and nucleotide metabolism. It is also believed that these findings are related to the chemical stimulation induced by thermal degradation and the ongoing catalysis of enzyme responses to drought stress. The facts presented above will give a scientific basis for the selection of FG drying processes, as well as helpful references for increasing the nutritional quality of processed FG. Full article
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16 pages, 1889 KiB  
Article
Untargeted Metabolomics Reveals Distinct Anthocyanin Profiles in Napier Grass (Pennisetum purpureum Schumach.) Cultivars
by Zhi-Yue Wang, Pei-Yin Lin, Chwan-Yang Hong, Kevin Chi-Chung Chou and Ting-Jang Lu
Foods 2025, 14(15), 2582; https://doi.org/10.3390/foods14152582 - 23 Jul 2025
Viewed by 275
Abstract
Plant secondary metabolites regulate plant growth and serve as valuable pharmaceutical resources. Napier grass (Pennisetum purpureum Schumach.), a Poaceae species, shows potential as a functional food. In this study, we employed high-resolution mass spectrometry combined with a data-independent acquisition (DIA) strategy for [...] Read more.
Plant secondary metabolites regulate plant growth and serve as valuable pharmaceutical resources. Napier grass (Pennisetum purpureum Schumach.), a Poaceae species, shows potential as a functional food. In this study, we employed high-resolution mass spectrometry combined with a data-independent acquisition (DIA) strategy for the untargeted detection of anthocyanins, a group of secondary metabolites, in napier grass. Clear MS2 fragmentation patterns were observed for anthocyanins, characterized by diagnostic aglycone signals and sequential losses of hexosyl (C6H10O5), deoxyhexosyl (C6H10O4), pentosyl (C5H8O4), and p-coumaroyl groups (C9H8O3). Based on matching with authentic standards and an in-house database, ten anthocyanins were identified, seven of which were newly reported in napier grass. In a single-laboratory validation analysis, both absolute and semi-quantitative results reliably reflected the specific distribution of metabolites across different cultivars and plant organs. The purple cultivar (TS5) exhibited the highest anthocyanin content, with the cyanidin 3-O-glucoside content reaching 5.0 ± 0.5 mg/g, whereas the green cultivar (TS2), despite its less pigmented appearance, contained substantial amounts of malvidin 3-O-arabinoside (0.7 ± <0.1 mg/g). Flavonoid profiling revealed that monoglycosylated anthocyanins were the dominant forms in floral tissues. These findings shed light on napier grass metabolism and support future Poaceae breeding and functional food development. Full article
(This article belongs to the Section Foodomics)
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14 pages, 870 KiB  
Article
Evaluation of Packaging Effects on the Phenolic Profile and Sensory Characteristics of Extra Virgin Olive Oil During Storage Using Liquid Chromatography Coupled with Mass Spectrometry
by Mohamed M. Abuhabib, Francesc M. Campins-Machado, Julián Lozano-Castellón, Antònia Ninot, Agustí Romero-Aroca, Rosa M. Lamuela-Raventós, Maria Pérez and Anna Vallverdú-Queralt
Foods 2025, 14(14), 2532; https://doi.org/10.3390/foods14142532 - 19 Jul 2025
Viewed by 424
Abstract
The health benefits of extra virgin olive oil (EVOO), including improved cardiovascular health and metabolic function, are linked to its phenolic content. This study evaluated how storage duration and packaging affect the phenolic composition and sensory quality of Corbella EVOO. Oils were analyzed [...] Read more.
The health benefits of extra virgin olive oil (EVOO), including improved cardiovascular health and metabolic function, are linked to its phenolic content. This study evaluated how storage duration and packaging affect the phenolic composition and sensory quality of Corbella EVOO. Oils were analyzed at production and after 6 and 12 months of storage in two types of packaging: bag-in-box; stainless steel containers with a nitrogen headspace. UPLC-MS/MS profiling quantified 23 phenolic compounds, predominantly secoiridoids such as oleuropein and ligstroside aglycones. Oleuropein aglycone increased over time, whereas ligstroside aglycone peaked mid-storage before declining, likely converting to oleocanthal. Lignans and flavonoids degraded during storage, although luteolin increased, potentially due to glucoside hydrolysis. Bag-in-box packaging better preserved phenolic content than stainless steel. A sensory analysis corroborated the chemical findings, with oils stored in stainless steel showing greater reductions in pungency and astringency. A Pearson correlation linked bitterness with oleuropein aglycone (r = 0.44) and oleacein (r = 0.66), pungency with oleocanthal (r = 0.81), and astringency with oleacein (r = 0.86) and oleocanthal (r = 0.71). These findings highlight the importance of packaging in preserving the phenolic composition responsible for the sensory qualities of EVOO over time. Full article
(This article belongs to the Special Issue Application of Mass Spectrometry-Based Omics and Chemometrics in Food)
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16 pages, 2327 KiB  
Article
Analysis of Protein Degradation and Umami Peptide Release Patterns in Stewed Chicken Based on Proteomics Combined with Peptidomics Approach
by Lei Cai, Qiuyu Zhu, Lili Zhang, Ruiyi Zheng, Baoguo Sun and Yuyu Zhang
Foods 2025, 14(14), 2497; https://doi.org/10.3390/foods14142497 - 16 Jul 2025
Viewed by 327
Abstract
Proteomics combined with peptidomics approaches were used to analyze the protein degradation and the release pattern of umami peptides in stewed chicken. The results showed that a total of 422 proteins were identified, of which 273 proteins consistently existed in samples stewed for [...] Read more.
Proteomics combined with peptidomics approaches were used to analyze the protein degradation and the release pattern of umami peptides in stewed chicken. The results showed that a total of 422 proteins were identified, of which 273 proteins consistently existed in samples stewed for 0–5 h. Myosin heavy chain exhibited the highest abundance (26.29–30.26%) throughout the stewing process. The proportion of proteins under 20 kDa increased progressively with the duration of stewing and reached 61% at 4–5 h of stewing. A total of 8018 peptides were detected in the soup samples, and 2323 umami peptides were identified using the prediction platforms iUmami-SCM, UMPred-FRL, Umami_YYDS, and TastePertides-DM. Umami peptides derived from titin (accession number A0A8V0ZZ81) were determined to be the most abundant, accounting for 24% of the total umami peptides, and Val534 and Lys33639 were the key N-terminal and C-terminal amino acids of these umami peptides. Abundance analysis showed that the umami peptides KK16 and SK18 ranked among the top 5 in the samples stewed for 0–5 h, and they were most abundant in the 3 h stewed samples. The results obtained will provide data support for promoting the industrialization of high-quality chicken soup products. Full article
(This article belongs to the Section Foodomics)
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18 pages, 6714 KiB  
Article
Metabolomics and Sensory Evaluation Reveal the Aroma and Taste Profile of Northern Guangdong Black Tea
by Jialin Chen, Binghong Liu, Yide Zhou, Jiahao Chen, Yanchun Zheng, Hui Meng, Xindong Tan, Peng Zheng, Binmei Sun, Hongbo Zhao and Shaoqun Liu
Foods 2025, 14(14), 2466; https://doi.org/10.3390/foods14142466 - 14 Jul 2025
Viewed by 453
Abstract
The sensory quality of black tea is intrinsically linked to cultivar genetics, yet comprehensive characterization of flavor compounds in emerging northern Guangdong black tea (NGBT) remains limited. This study employed high-performance liquid chromatography-ultraviolet (HPLC-UV) and headspace solid-phase microextraction coupled with GC-MS (HS-SPME-GC-MS) to [...] Read more.
The sensory quality of black tea is intrinsically linked to cultivar genetics, yet comprehensive characterization of flavor compounds in emerging northern Guangdong black tea (NGBT) remains limited. This study employed high-performance liquid chromatography-ultraviolet (HPLC-UV) and headspace solid-phase microextraction coupled with GC-MS (HS-SPME-GC-MS) to analyze non-volatile and volatile compounds in five NGBT cultivars—Jinshahong (JSH), Danxia No.1 (DXY), Danxia No.2 (DXE), Yingde Black Tea (QTZ), and Yinghong No.9 (YHJ)—alongside sensory evaluation. Orthogonal partial least squares-discriminant analysis (OPLS-DA) identified key non-volatile discriminants (VIP > 1) ranked by contribution: total catechins > simple catechins > CG > EGCG > ester catechins > EGC. HS-SPME-GC-MS detected 97 volatiles, with eight aroma-active compounds exhibiting OAV > 1 and VIP > 1: Geraniol > Methyl salicylate > Linalool > β-Myrcene > Benzyl alcohol > (Z)-Linalool Oxide > Phenethyl alcohol > (Z)-Jasmone. These compounds drive cultivar-specific aromas in NGBTs. Findings establish a theoretical framework for evaluating cultivar-driven flavor quality and provide novel insights for targeted breeding and processing optimization of NGBTs. Full article
(This article belongs to the Section Foodomics)
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15 pages, 4388 KiB  
Article
Metabolomic Insights into Volatile Profiles and Flavor Enhancement of Spice-Smoked Chicken Wings
by Yajiao Zhao, Ye Guo, Danni Zhang, Quanlong Zhou, Xiaoxiao Feng and Yuan Liu
Foods 2025, 14(13), 2270; https://doi.org/10.3390/foods14132270 - 26 Jun 2025
Viewed by 407
Abstract
Traditional smoking techniques, while historically valued for preservation and flavor enhancement, face limitations in aromatic diversity and safety, prompting exploration of spice-derived alternatives to meet modern culinary demands. This study explores the volatile compound profiles and aroma modulation of chicken wings smoked with [...] Read more.
Traditional smoking techniques, while historically valued for preservation and flavor enhancement, face limitations in aromatic diversity and safety, prompting exploration of spice-derived alternatives to meet modern culinary demands. This study explores the volatile compound profiles and aroma modulation of chicken wings smoked with four spices—cardamom, rosemary, mint, and rose—using a novel, household-friendly smoking protocol. The method combines air fryer pre-cooking (180 °C, 16 min) with electric griddle-based smoke infusion, followed by HS-SPME/GC-TOF/MS, relative odor activity value (ROAV) calculations, and metabolomic analysis. A total of 314 volatile compounds were identified across five samples. Among them, 45 compounds demonstrated odor activity values (ROAV) ≥ 1, contributing to green, woody, floral, and sweet aroma attributes. Eucalyptol displayed the highest ROAV (2543), underscoring its dominant sensory impact. Metabolomic profiling revealed a general upregulation of differential volatiles post-smoking: terpenes were enriched in wings smoked with cardamom, rosemary, and mint, while aldehydes and alcohols predominated in rose-smoked samples. An integrated screening based on ROAV and metabolomic data identified 24 key volatiles, including eucalyptol, β-myrcene, methanethiol, and α-pinene, which collectively defined the aroma signatures of spice-smoked wings. Spice-specific aroma enrichment and sensory properties were evident: rosemary intensified woody–spicy notes, mint enhanced herbal freshness, and rose amplified floral attributes. The proposed method demonstrated advantages in safety, ease of use, and flavor customization, aligning with clean-label trends and supporting innovation in home-based culinary practices. Moreover, it facilitates the tailored modulation of smoked meat flavor profiles, thereby enhancing product differentiation and broadening consumer acceptance. Full article
(This article belongs to the Special Issue Foodomics Fifteen Years On From. Where Are We Now, What’s Next)
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17 pages, 3966 KiB  
Article
Integrated Metabolomic and Transcriptomic Analysis of Volatile Organic Compound Biosynthesis During Mung Bean (Vigna radiata) Seed Development
by Nan Xiang, Yihan Zhao, Bing Zhang, Honglin Chen and Xinbo Guo
Foods 2025, 14(13), 2183; https://doi.org/10.3390/foods14132183 - 22 Jun 2025
Viewed by 426
Abstract
Mung bean (Vigna radiata L.) is globally cultivated and has been widely used in the food industries. Other than nutrients, the composition of the volatile organic compounds (VOCs) often influences the quality of mung bean-based products. However, the dynamics of VOCs and [...] Read more.
Mung bean (Vigna radiata L.) is globally cultivated and has been widely used in the food industries. Other than nutrients, the composition of the volatile organic compounds (VOCs) often influences the quality of mung bean-based products. However, the dynamics of VOCs and the flavor changes during mung bean seed development remain unexplored. This study investigated the VOC and flavor composition in four mung bean varieties by integrating relative odor activity value (ROAV) evaluation and transcriptomic analysis. A total of 65 VOCs were identified, with eucalyptol serving as a key maturity indicator in LL655 and SH-1, while nonanal contributed significantly to the characteristic beany flavor across all varieties. Transcriptomic analysis revealed four downregulated geranylgeranyl diphosphate synthase genes during seed development, leading to terpenoid accumulation patterns. Terpenoids, including trans-beta ocimene and gamma-terpinene, appeared to be regulated by transcription factors (TFs) from the RLK-Pelle, WRKY, AP2/ERF, bHLH, and bZIP families. Additionally, two MYB TFs showed potential roles in modulating the accumulation of phenylpropanoid/benzenoid derivatives. This study provides a comprehensive understanding of the VOC accumulation and flavor variation during mung bean seed development, enriches the knowledge of flavor chemistry in mung bean varieties, and facilitates a theoretical foundation for optimizing and developing mung bean-based products. Full article
(This article belongs to the Section Foodomics)
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18 pages, 8398 KiB  
Article
Application of Predictive Modeling and Molecular Simulations to Elucidate the Mechanisms Underlying the Antimicrobial Activity of Sage (Salvia officinalis L.) Components in Fresh Cheese Production
by Dajana Vukić, Biljana Lončar, Lato Pezo and Vladimir Vukić
Foods 2025, 14(13), 2164; https://doi.org/10.3390/foods14132164 - 20 Jun 2025
Viewed by 484
Abstract
Plant-derived materials from Salvia officinalis L. (sage) have demonstrated significant antimicrobial potential when applied during fresh cheese production. In this study, the mechanism of action of sage components against Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus was investigated through the development of [...] Read more.
Plant-derived materials from Salvia officinalis L. (sage) have demonstrated significant antimicrobial potential when applied during fresh cheese production. In this study, the mechanism of action of sage components against Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus was investigated through the development of predictive models that describe the influence of key parameters on antimicrobial efficacy. Molecular modeling techniques were employed to identify the major constituents responsible for the observed inhibitory activity. Epirosmanol, carvacrol, limonene, and thymol were identified as the primary compounds contributing to the antimicrobial effects during cheese production. The highest weighted predicted binding energy was observed for thymol against the KdpD histidine kinase from Staphylococcus aureus, with a value of −33.93 kcal/mol. To predict the binding affinity per unit mass of these sage-derived compounds against the target pathogens, machine learning models—including Artificial Neural Networks (ANN), Support Vector Machines (SVM), and Boosted Trees Regression (BTR)—were developed and evaluated. Among these, the ANN model demonstrated the highest predictive accuracy and robustness, showing minimal bias and a strong coefficient of determination (R2 = 0.934). These findings underscore the value of integrating molecular modeling and machine learning approaches for the identification of bioactive compounds in functional food systems. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Food Science)
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12 pages, 1972 KiB  
Article
Comparing the Metabolic Characteristics of Hyacinth Bean (Lablab purpureus L.) Seeds from Five Local Varieties by UHPLC-QE HF HRMS
by Li Yu, Zhiwu Huang, Luzhao Pan, Hengyu Meng, Weimin Zhu and Jun Yan
Foods 2025, 14(11), 1939; https://doi.org/10.3390/foods14111939 - 29 May 2025
Viewed by 567
Abstract
Hyacinth bean seeds are a good source of vegetable protein and have great potential for medicinal development. However, their metabolic characteristics are unclear. Therefore, in this study, we conducted non-targeted metabolomics research on hyacinth bean seeds from local varieties using ultra-high-performance liquid chromatography [...] Read more.
Hyacinth bean seeds are a good source of vegetable protein and have great potential for medicinal development. However, their metabolic characteristics are unclear. Therefore, in this study, we conducted non-targeted metabolomics research on hyacinth bean seeds from local varieties using ultra-high-performance liquid chromatography combined with high-field quadrupole orbital trap high-resolution mass spectrometry (UHPLC-QE HF HRMS) and evaluated their antioxidant properties. A total of 745 metabolites were identified, including many bioactive medicinal compounds such as chikusetsusaponin IVa, pipecolic acid, and genistin. The seed coat color and origin of hyacinth bean seeds have significant impacts on their metabolic characteristics. Compared with the other four hyacinth beans, the Chongming white hyacinth bean (SCLW) has a higher medicinal value, with glycitin, finsenoside Ro, diferuloyl glycerol, isopongflavone, procyanidin B2, and pratensein speculated to be its characteristic metabolites. DPPH and FRAP assays showed that the antioxidant activity of SCLW was significantly higher than that of the other four hyacinth bean seeds, and 11 metabolites related to antioxidant activity were identified. These findings enrich our knowledge of the metabolites in hyacinth bean seeds, which is of great significance for hyacinth bean cultivation according to local conditions and for the improvement of variety quality. Full article
(This article belongs to the Section Foodomics)
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15 pages, 2326 KiB  
Article
Sensory and Instrumental Characterization of Parmigiano Reggiano Protected Designation of Origin Cheese Obtained from Milk of Cows Fed Fresh Herbage vs. Dry Hay
by Mara Antonia Gagliano, Matilde Tura, Francesca Soglia, Chiara Cevoli, Sara Barbieri, Giacomo Braschi, Alessandra Bendini, Tullia Gallina Toschi, Massimiliano Petracci and Enrico Valli
Foods 2025, 14(10), 1781; https://doi.org/10.3390/foods14101781 - 17 May 2025
Viewed by 481
Abstract
Using a multi-analytical approach, this investigation characterized Parmigiano Reggiano PDO cheese produced with milk from dairy cows fed different diets. Ten samples of Parmigiano Reggiano PDO cheese, aged for 24 months, were produced with milk from dairy cows fed only dry hay (P-DH; [...] Read more.
Using a multi-analytical approach, this investigation characterized Parmigiano Reggiano PDO cheese produced with milk from dairy cows fed different diets. Ten samples of Parmigiano Reggiano PDO cheese, aged for 24 months, were produced with milk from dairy cows fed only dry hay (P-DH; N = 6) or a diet with part of the dry hay replaced with fresh herbage (P-FF; N = 4). Instrumental (Flash GC-FID) analysis of the volatile fraction, image analyses, and sensory quantitative descriptive analysis (QDA®) were carried out. The Parmigiano Reggiano cheese belonging to the P-FF group showed a higher intensity of yellow than P-DH for both sensory and image analyses. Regarding the volatile profiles, no differences were observed related to the two experimental groups, while sensory analyses allowed for some discrimination, in particular color and aroma attributes. Instrumental and sensory characterization can be used to obtain a unique analytical profile for Parmigiano Reggiano PDO cheeses produced with milk from dairy cows fed different forage sources and help to define the quality and authenticity of this typical high-value food product. Full article
(This article belongs to the Special Issue Foodomics Fifteen Years On From. Where Are We Now, What’s Next)
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23 pages, 3172 KiB  
Article
Optimization of Protein Extraction from Rapeseed Oil Cake by Dephenolization Process for Scale-Up Application Using Artificial Neural Networks
by Branislava Đermanovć, Jelena Vujetić, Tea Sedlar, Danka Dragojlović, Ljiljana Popović, Predrag Kojić, Pavle Jovanov and Bojana Šarić
Foods 2025, 14(10), 1762; https://doi.org/10.3390/foods14101762 - 16 May 2025
Cited by 2 | Viewed by 816
Abstract
Rapeseed proteins, due to their quality and wide availability, have great potential for application in human nutrition. However, their high content of antinutritional compounds poses significant economic and environmental challenges for food industry applications. To overcome these obstacles, various extraction and modification techniques, [...] Read more.
Rapeseed proteins, due to their quality and wide availability, have great potential for application in human nutrition. However, their high content of antinutritional compounds poses significant economic and environmental challenges for food industry applications. To overcome these obstacles, various extraction and modification techniques, including enzymatic and ultrasound-assisted methods, were used to enhance protein functionality and improve both nutritional and sensory properties. In this study, the effects of dephenolization on the structural, physicochemical, and functional properties of rapeseed protein isolate obtained from defatted rapeseed cake were investigated through four different protocols. All obtained protein isolates (PIs) exhibited high protein purity (above 65%), with a notable difference in extraction yield. Furthermore, the extraction process was optimized using an artificial neural network (ANN) model, which demonstrated high predictive performance. The optimal extraction conditions for the dephenolization of rapeseed oil cake were 84% ethanol concentration, a solid-to-liquid ratio of 1/60 w/v, and 15 min of ultrasound treatment, resulting in an impressive protein purity of 90.68% with a yield of 29.17%. The obtained proteins were further characterized and compared in terms of protein profile (FTIR and SDS-PAGE), amino acid composition, solubility, and digestibility. The protein isolate (PI) obtained under optimized conditions displayed superior functional properties, underscoring the relevance and necessity of a data-driven, mathematical approach for scale-up and industrial implementation. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Food Science)
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18 pages, 5494 KiB  
Article
Transcriptomic Profiling Uncovers Molecular Basis for Sugar and Acid Metabolism in Two Pomegranate (Punica granatum) Varieties
by Ding Ke, Yilong Zhang, Yingfen Teng and Xueqing Zhao
Foods 2025, 14(10), 1755; https://doi.org/10.3390/foods14101755 - 15 May 2025
Viewed by 440
Abstract
Soluble sugars and organic acids constitute the primary flavor determinants in fruits and elucidating their metabolic mechanisms provides crucial theoretical foundations for fruit breeding practices and food industry development. Through integrated physiological and transcriptomic analysis of pomegranate varieties ‘Sharp Velvet’ with high acid [...] Read more.
Soluble sugars and organic acids constitute the primary flavor determinants in fruits and elucidating their metabolic mechanisms provides crucial theoretical foundations for fruit breeding practices and food industry development. Through integrated physiological and transcriptomic analysis of pomegranate varieties ‘Sharp Velvet’ with high acid content and ‘Azadi’ with low acid content, this study demonstrated that the differences in flavor between the two varieties were mainly caused by differences in citric acid content rather than in soluble sugar content. Transcriptome profiling identified 11 candidate genes involved in sugar and acid metabolism, including three genes associated with soluble sugar metabolism (FBA1, SS, and SWEET16) and eight genes linked to organic acid metabolism (ADH1, GABP1, GABP2, GABP3, GABP4, ICL, ME1, and PDC4). These data indicated that differences in citric acid content between the two varieties mainly stemmed from differences in the regulation of the citric acid degradation pathway, which relies mainly on the γ-aminobutyric acid (GABA) branch rather than the isocitric acid lyase (ICL) pathway. Citric acid accumulation in pomegranate fruit was driven by metabolic fluxes rather than vesicular storage capacity. Weighted gene co-expression network analysis (WGCNA) uncovered a significant citric acid content associated module (r = −0.72) and predicted six core transcriptional regulators (bHLH42, ERF4, ERF062, WRKY6, WRKY23, and WRKY28) within this network. Notably, bHLH42, ERF4, and WRKY28 showed significant positive correlations with citric acid content, whereas ERF062, WRKY6, and WRKY23 demonstrated significant negative correlations. Our findings provide comprehensive insights into the genetic architecture governing soluble sugars and organic acids homeostasis in pomegranate, offering both a novel mechanistic understanding of fruit acidity regulation and valuable molecular targets for precision breeding of fruit quality traits. Full article
(This article belongs to the Special Issue Foodomics Approaches—Technologies and Their Applications)
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15 pages, 3721 KiB  
Article
Integrated Analysis of the Transcriptome and Metabolome Reveals the Network Regulating Fruit Taste in Sponge Gourd (Luffa cylindrica)
by Yaqian Chai, Wenjing Qiu, Zhikun Li, Luyao Gao, Wenqi Dong, Peng Zhang, Shengjun Zhou, Xin Wang, Yuqiang Zhu and Yuyan Sun
Foods 2025, 14(10), 1753; https://doi.org/10.3390/foods14101753 - 15 May 2025
Viewed by 393
Abstract
Sponge gourd fruit is highly favored by consumers because of its nutritional and medicinal properties. Continuous increases in living standards have led to an increase in the demand for high-quality fruits and vegetables. Hence, we explored the mechanisms that regulate fruit taste development. [...] Read more.
Sponge gourd fruit is highly favored by consumers because of its nutritional and medicinal properties. Continuous increases in living standards have led to an increase in the demand for high-quality fruits and vegetables. Hence, we explored the mechanisms that regulate fruit taste development. Specifically, two sponge gourd materials, ZS203 (GT) and ZAAS-106 (BT), which differ in fruit taste, were selected for transcriptomic and metabolomic analyses. Ascorbic acid, soluble solids, and crude protein contents were significantly higher in GT than in BT. Similarly, the lysine, phenylalanine, and tryptophan contents were higher in GT than in BT (1.48-, 1.60-, and 1.38 times higher, respectively). Transcriptomic analysis of GT and BT fruits identified 1821 upregulated and 1185 downregulated differentially expressed genes (DEGs) in GT, while metabolomic analysis detected 25 upregulated differentially accumulated metabolites (DAMs) and 28 downregulated DAMs in GT. A correlation analysis suggested that DAMs and DEGs related to vitamin B6 metabolism, tryptophan metabolism, and phenylalanine metabolism contribute to the differences in sponge gourd fruit taste; a potential mechanism underlying this diversity was proposed. Additionally, expression data for the 15 DEGs were consistent between transcriptomic and qRT-PCR analyses. Notably, this study revealed a potential mechanism for regulating differences in sponge gourd fruit taste, with possible implications for breeding novel varieties with optimized fruit taste. Full article
(This article belongs to the Special Issue Application of Metabolomics in Enhancing Food Texture and Flavor)
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17 pages, 3301 KiB  
Article
Food Iminosugars and Related Synthetic Derivatives Shift Energy Metabolism and Induce Structural Changes in Colon Cancer Cell Lines
by Thomas Montebugnoli, Charlotte Grootaert, Alessandra Bordoni, Andreja Rajković, Elien Alderweireldt, Jeltien Rombaut, Sofie L. De Maeseneire, John Van Camp and Maarten Lieven De Mol
Foods 2025, 14(10), 1713; https://doi.org/10.3390/foods14101713 - 12 May 2025
Viewed by 576
Abstract
Iminosugars have a carbohydrate-like backbone in which the ring oxygen is replaced by nitrogen. They are naturally found in foods such as rice, buckwheat, mulberries, and fermented vegetables, and are reported to exert anti-hyperlipidemic and anti-hyperglycemic effects due to the inhibition of cellular [...] Read more.
Iminosugars have a carbohydrate-like backbone in which the ring oxygen is replaced by nitrogen. They are naturally found in foods such as rice, buckwheat, mulberries, and fermented vegetables, and are reported to exert anti-hyperlipidemic and anti-hyperglycemic effects due to the inhibition of cellular glycosidases. This mechanism suggests their potential role in cancer treatment and prevention. In this study, two natural iminosugars, D-fagomine (FGM) and 1-deoxynojirimycin (DNJ), and their synthetic derivatives were screened for potential anticancer properties using Caco-2 and HCT-116 cells as models for the early and late stages of colon cancer, respectively. Iminosugars were found to decrease cell viability, with effects varying based on the type of iminosugar, cell type, growth condition (glucose concentration), exposure time (1 vs. 13 days), and tissue architecture (monolayer vs. spheroid). The combined use of innovative techniques, such as IncuCyte® live cell imaging and Seahorse real-time cellular metabolic analysis, and microscopic observation after staining enabled us to detect changes in substrate utilization for energy metabolism, including increased glycolysis and alterations in lipid and glycogen stores. The evidence that iminosugars, both natural and synthetic, influence cellular bioenergetics paves the way for their potential use in various applications, including cancer treatment. Full article
(This article belongs to the Special Issue Foodomics Fifteen Years On From. Where Are We Now, What’s Next)
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16 pages, 1535 KiB  
Article
Exploratory Genomic Marker Analysis of Virulence Patterns in Listeria monocytogenes Human and Food Isolates
by Valeria Russini, Maria Laura De Marchis, Cinzia Sampieri, Cinzia Onorati, Piero Zucchitta, Paola De Santis, Bianca Maria Varcasia, Laura De Santis, Alexandra Chiaverini, Antonietta Gattuso, Annarita Vestri, Laura Gasperetti, Roberto Condoleo, Luigi Palla and Teresa Bossù
Foods 2025, 14(10), 1669; https://doi.org/10.3390/foods14101669 - 9 May 2025
Viewed by 469
Abstract
Listeria monocytogenes causes listeriosis, a severe foodborne disease with high mortality. Contamination with it poses significant risks to food safety and public health. Notably, genetic characteristic differences exist between strains causing human infections and those found in routine food inspections. This study examined [...] Read more.
Listeria monocytogenes causes listeriosis, a severe foodborne disease with high mortality. Contamination with it poses significant risks to food safety and public health. Notably, genetic characteristic differences exist between strains causing human infections and those found in routine food inspections. This study examined the genotypic factors influencing the pathogenicity of L. monocytogenes, focusing on virulence gene profiles and key integrity genes like inlA to explain these divergences. The dataset included 958 strains isolated from human, food, and environmental samples. Whole-genome sequencing identified virulence genes, and principal component analysis (PCA) examined 92 virulence genes and inlA integrity to uncover potentially pathogenic patterns. The results highlight differences in virulence characteristics between strains of different origins. The integrity of inlA and genes such as inlD, inlG, and inlL were pivotal to pathogenicity. Strains with premature stop codons (PMSCs) in inlA, associated with reduced virulence, accounted for a low percentage of human cases but over 30% of food isolates. Sequence types (STs) like ST121, ST580, and ST199 showed unique profiles, while ST9, dominant in food, occasionally caused human cases, posing risks to vulnerable individuals. This research highlights the complexity of the pathogenicity of L. monocytogenes and emphasizes the importance of genomic surveillance for effective risk assessment. Full article
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