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Foodomics Fifteen Years On From. Where Are We Now, What’s...
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Foodomics Fifteen Years On From. Where Are We Now, What’s Next

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Foodomics".

Deadline for manuscript submissions: closed (15 March 2025) | Viewed by 9895

Special Issue Editors

Prof. Dr. Alessandra Bordoni

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Guest Editor
Department of Agro-Food Sciences and Technologies (DISTAL), University of Bologna, piazza Goidanich, 60, 47521 Cesena, FC, Italy
Interests: human nutrition; nutritional biochemistry; fatty acids; in vitro digestion; bioavailability; nutrigenomics; bioactive compounds
Special Issues, Collections and Topics in MDPI journals
Dr. Elena Babini

E-Mail Website
Guest Editor
Department of Agro-Food Sciences and Technologies (DISTAL), University of Bologna, piazza Goidanich, 60, 47521 Cesena, FC, Italy
Interests: foodomics; metabolomics; protein chemistry; protein purification; alternative proteins; antioxidants
Prof. Dr. Francesco Capozzi

E-Mail Website
Guest Editor
Department of Agricultural and Food Sciences, Alma Mater Studiorum Università di Bologna, Cesena, Italy
Interests: foodomics; biomarkers; metabolomics; NMR spectroscopy; food structure; in vitro digestion modelling; food kinetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

There is much discussion about the classification of foods for nutritional purposes. Do we need FoodOmics to correctly classify foods based on their composition and structure?

Much of the scientific evidence explaining the link between nutrition and health requires biomarkers to demonstrate that the consumption of foods reported in questionnaires corresponds to actual consumption. Do we need FoodOmics to effectively find robust biomarkers?

Food technologists point out that rheological properties are very different between animal and plant ingredients (e.g., proteins and fats). In short, alternative sources could become alternative nutrients, provided that more information is collected on their nutritional and technological properties. The methodological approach of FoodOmics can certainly shed light on these aspects.

The structure of a food source is complicated to measure and quantitatively correlate with the digestibility, bioaccessibility and bioavailability of nutrients. The FoodOmics approach, because its mission is to provide a high-definition description of food, can bridge this gap between the present and future of precision nutrition, focusing its holistic vision on the structural aspect.

We would like to invite researchers to participate in this Special Issue by presenting a new and updated knowledge base on the above-mentioned aspects. Both original research papers and critical reviews are welcome.

Potential topics include, but are not limited to, the following:

  • FoodOmics for the molecular composition of foods;
  • FoodOmics for the bioaccessibility and bioavailability of nutrients;
  • FoodOmics and health;
  • FoodOmics and alternative sources.

Prof. Dr. Alessandra Bordoni
Dr. Elena Babini
Prof. Dr. Francesco Capozzi
Guest Editors

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. Foods is an international peer-reviewed open access semimonthly 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 2900 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

  • FoodOmics
  • alternative nutrients
  • biomarkers
  • bioaccessibility
  • bioavailability
  • food categories
  • food processing

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Published Papers (6 papers)

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18 pages, 1027 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
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)
14 pages, 4561 KiB  
Article
Proteomics-Based Investigation of Sexual Dimorphism in Swim Bladder Texture of Chu’s Croaker (Nibea coibor)
by Haoran Zhang, Jiali Lin, Haoji Guo, Xianda He, Wanying Jiang, Lin Yan, Kuoqiu Yan, Xiaobo Wen and Fan Lin
Foods 2025, 14(9), 1586; https://doi.org/10.3390/foods14091586 - 30 Apr 2025
Viewed by 279
Abstract
The swim bladder of Chu’s croaker (Nibea coibor) is an expensive food with high texture requirements. In this study, we found that male swim bladder had better toughness than female. To explore the main determining factor affecting texture properties of swim [...] Read more.
The swim bladder of Chu’s croaker (Nibea coibor) is an expensive food with high texture requirements. In this study, we found that male swim bladder had better toughness than female. To explore the main determining factor affecting texture properties of swim bladder, a comparison of proximate composition, collagen microstructure, and proteomics was carried out between male and female swim bladders. Results indicated that it should be collagen microstructure mainly affecting the texture characteristics of swim bladder, rather than the composition. The collagen fibers in male swim bladder were significantly more uniform and regular than female. By proteomics analysis, it was further discovered that collagen XII was the most significantly up-regulated protein in the male swim bladder and may be crucial in morphology of collagen fibers. In summary, collagen XII was identified to be a potential key molecule affecting the texture of the swim bladder, mainly through regulating properties of collagen fibers. This study contributes to a deeper understanding of the structural characteristics of swim bladder collagen and provides critical molecular targets for the regulation of texture in swim bladder. 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, 1221 KiB  
Article
Comparative Analysis of Fatty Acid Bioaccessibility in Commercial Marine Oil Supplements: An In Vitro Integrated Analytical Study
by Thomas Montebugnoli, Giorgia Antonelli, Elena Babini, Ester Maria Vasini, Francesca Danesi, Sigrún Huld Jónasdóttir, María Gudjónsdóttir, Francesco Capozzi and Alessandra Bordoni
Foods 2024, 13(24), 4177; https://doi.org/10.3390/foods13244177 - 23 Dec 2024
Viewed by 1442
Abstract
Zooplankton such as copepods and krill are currently used to produce marine oil supplements, with the aim of helping consumers achieve the recommended intake of n-3 long chain polyunsaturated fatty acids (n-3 LC-PUFAs). Oils from lower trophic levels differ from fish oil in [...] Read more.
Zooplankton such as copepods and krill are currently used to produce marine oil supplements, with the aim of helping consumers achieve the recommended intake of n-3 long chain polyunsaturated fatty acids (n-3 LC-PUFAs). Oils from lower trophic levels differ from fish oil in the distribution of lipids into different classes, and this can influence the bioaccessibility of fatty acids, i.e., the percentage of fatty acids that are released into the intestine in a form that can be absorbed by enterocytes. We evaluated fatty acid release after in vitro digestion in four commercial marine oil supplements containing fish, krill and Calanus finmarchicus oils using two different analytical approaches, TLC-FID and 1H-NMR spectroscopy. The results clearly indicated that the release of free fatty acids (FFAs) after simulated digestion mainly depends on the oil source and is mainly related to the partitioning of lipids into different classes. In fact, the lowest FFA release was detected in Calanus oils, which contain high amounts of wax esters. The different release of FFAs, which appeared secondarily related to encapsulation, can modulate the absorption and blood concentration of the administered n-3 LC-PUFAs and therefore their efficacy. This may partly explain the inconsistencies in intervention studies using marine oil supplements. 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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19 pages, 3891 KiB  
Article
A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua
by Alessandra Tata, Andrea Massaro, Brunella Miano, Sara Petrin, Pietro Antonelli, Arianna Peruzzo, Alessandra Pezzuto, Michela Favretti, Marco Bragolusi, Carmela Zacometti, Carmen Losasso and Roberto Piro
Foods 2024, 13(12), 1912; https://doi.org/10.3390/foods13121912 - 18 Jun 2024
Cited by 4 | Viewed by 1597
Abstract
Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in [...] Read more.
Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms. 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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15 pages, 1328 KiB  
Article
Fermentation of Orange Peels by Lactic Acid Bacteria: Impact on Phenolic Composition and Antioxidant Activity
by María del Carmen Razola-Díaz, Soumi De Montijo-Prieto, Eduardo Jesús Guerra-Hernández, María Jiménez-Valera, Alfonso Ruiz-Bravo, Ana María Gómez-Caravaca and Vito Verardo
Foods 2024, 13(8), 1212; https://doi.org/10.3390/foods13081212 - 16 Apr 2024
Cited by 4 | Viewed by 3881
Abstract
Orange processing generates peel by-products rich in phenolic compounds, particularly flavanones like hesperidin and narirutin, offering potential health benefits. Utilizing these by-products is of significant interest in supporting Spain’s circular bioeconomy. Therefore, the aim of this study was to investigate the fermentation of [...] Read more.
Orange processing generates peel by-products rich in phenolic compounds, particularly flavanones like hesperidin and narirutin, offering potential health benefits. Utilizing these by-products is of significant interest in supporting Spain’s circular bioeconomy. Therefore, the aim of this study was to investigate the fermentation of orange peels by different lactic acid bacteria (LAB) strains and its impact on phenolic composition and antioxidant activity. Three different LAB strains, two Lactiplantibacillus plantarum, and one Levilactobacillus brevis were utilized. The phenolic compounds were measured by HPLC-ESI-TOF-MS, and antioxidant activity was assessed using DPPH and ABTS methods. The growth of the LAB strains varied, showing initial increases followed by gradual declines, with strain-specific patterns observed. Medium acidification occurred during fermentation. A phenolic analysis revealed an 11% increase in phenolic acids in peels fermented by La. plantarum CECT 9567-C4 after 24 h, attributed to glycosylation by LAB enzymes. The flavonoid content exhibited diverse trends, with Le. brevis showing an 8% increase. The antioxidant assays demonstrated strain- and time-dependent variations. Positive correlations were found between antioxidant activity and total phenolic compounds. The results underscore the importance of bacterial selection and fermentation time for tailored phenolic composition and antioxidant activity in orange peel extracts. LAB fermentation, particularly with La. plantarum CECT 9567 and Le. brevis, holds promise for enhancing the recovery of phenolic compounds and augmenting antioxidant activity in orange peels, suggesting potential applications in food and beverage processing. 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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5 pages, 194 KiB  
Viewpoint
Redefining Protein Quality: Integrating Health Outcomes and Environmental Impacts in the Plant-Animal Protein Debate
by Francesco Visioli
Foods 2024, 13(24), 4128; https://doi.org/10.3390/foods13244128 - 20 Dec 2024
Cited by 1 | Viewed by 1941
Abstract
There is an ongoing debate about the relative merits of plant-based versus animal-based protein sources in terms of human health outcomes and environmental impacts. This viewpoint article reviews and synthesizes the current evidence comparing plant and animal protein sources on measures of human [...] Read more.
There is an ongoing debate about the relative merits of plant-based versus animal-based protein sources in terms of human health outcomes and environmental impacts. This viewpoint article reviews and synthesizes the current evidence comparing plant and animal protein sources on measures of human health like cardiovascular disease, cancer, and mortality risk, as well as environmental factors like greenhouse gas emissions, water use, and land requirements. Overall, greater consumption of plant protein sources like legumes, nuts, seeds, and whole grains is associated with reduced risks of cardiovascular diseases, some cancers, and mortality, especially compared to red and processed meats. Crucially, these health benefits align with the dramatically lower environmental footprints of plant proteins across measures like emissions, water use, and land use. However, evidence is mixed for some health outcomes, and more research is still needed. While blanket recommendations should be avoided, the convergence of health and environmental advantages suggests future dietary guidance should emphasize shifting toward more plant-based protein sources. However, evaluations must consider specific foods rather than broad categorizations. New protein production methods like precision fermentation may also reduce environmental impacts while maintaining adequate nutrition. 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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