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Metabolomics of Human Nutrition: The Dot of Human Nutrition and...
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Metabolomics of Human Nutrition: The Dot of Human Nutrition and the Circle of Soil, Plants, Animals and Microbes in Relation to It, 2nd Edition

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Nutrition and Metabolism".

Deadline for manuscript submissions: 21 May 2026 | Viewed by 5767

Special Issue Editor

Prof. Dr. Shoma Berkemeyer

E-Mail Website
Guest Editor
Faculty of Agricultural Sciences and Landscape Architecture, Osnabrueck University of Applied Sciences, Am Kruempel 31, 49090 Osnabrueck, Germany
Interests: nutritional sciences
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Metabolites is dedicated to exploring the metabolomics of human nutrition in health and disease, as well as its intricate connections to soil science, botany with crop science, zoology with animal husbandry, and the diverse microbial ecosystems of the biosphere. While various hypotheses exist regarding the interplay between the metabolic processes within the human body (micro-cosmos) and those in the broader biosphere (macro-cosmos), a comprehensive and systematic knowledge base on this subject is still lacking.

To bridge this gap, this Special Issue aims to leverage metabolomics both as an independent analytical approach and within the broader omics framework. The metabolome offers a highly integrative and dynamic perspective on human nutrition, providing the basis for in-depth analyses and systemic syntheses that encompass both key disciplinary insights and interdisciplinary linkages.

We invite contributions that focus on the metabolomics of human nutrition from a range of scientific disciplines, including physiology, anatomy, dietetics, toxicology, food science, pathophysiology, microbiology, microbiome research, pharmacokinetics, and biochemistry. Additionally, we encourage submissions that investigate the crucial link between human nutrition and environmental sciences—specifically, metabolomics research connecting human nutrition to soil science, botany with crop science, and zoology with animal husbandry, as well as on microbial ecosystems spanning marine and freshwater bodies, the atmosphere, and terrestrial landscapes.

This Special Issue seeks to foster a holistic, circular understanding of human nutrition by integrating perspectives from both specialized fields and interdisciplinary research. We welcome original research articles, reviews, and methodological advances that contribute to this comprehensive perspective on human nutrition and its interconnectedness with the biosphere.

Prof. Dr. Shoma Berkemeyer
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 250 words) can be sent to the Editorial Office for assessment.

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

  • human nutrition
  • metabolomics
  • physiology
  • biochemistry
  • dietetics
  • pathophysiology
  • soil science
  • crop science
  • animal husbandry
  • microbes

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Published Papers (3 papers)

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19 pages, 3184 KB  
Article
Metabolome and Essential Element Analyses of Five Underutilized European Crops Reveal Their Nutritional Properties and Potential to Diversify the European Food System
by Mihail Angelov, Valentina Ivanova, Plamen Stoyanov, Rumen Mladenov, Tsvetelina Mladenova, Donika Gyuzeleva, Simona Zhelyazkova, Tzenka Radoukova, Krasimir Todorov, Stefka Bogdanova, Aleksandra Ivanova, Michael Wittenberg, Veselin Petrov and Tsanko Gechev
Metabolites 2025, 15(11), 720; https://doi.org/10.3390/metabo15110720 - 3 Nov 2025
Cited by 1 | Viewed by 1001
Abstract
Background/Objectives: People in the developed world tend to consume food that is rich in calories but lacks sufficient nutrients such as essential minerals, vitamins, and other health-promoting metabolites. At the same time, hunger and malnutrition are still problems in other countries. Therefore, various [...] Read more.
Background/Objectives: People in the developed world tend to consume food that is rich in calories but lacks sufficient nutrients such as essential minerals, vitamins, and other health-promoting metabolites. At the same time, hunger and malnutrition are still problems in other countries. Therefore, various forms of micronutrient deficiencies and diseases caused by unbalanced nutrition are global issues. Methods: In order to elucidate the beneficial potential of alternative food sources, we employed state-of-the-art UHPLC-MS and ICP-MS technologies to perform comprehensive metabolome and metallome analyses of five edible European plants, some of which are known as underutilized crops: Achillea millefolium, Agastache rugosa, Cercis siliquastrum, Crithmum maritimum, and Mespilus germanica. Results: This study reveals valuable nutritional properties such as high levels of essential amino acids, sugars, organic acids, health-promoting secondary metabolites, and essential microelements that are important for human diet. The analyzed samples indicate that A. millefolium, C. siliquastrum, and M. germanica could be marked as a viable source of beneficial flavonoids. In turn, both leaves and fruits of A. rugosa had elevated abundances of organic acids, along with A. millefolium and C. siliquastrum. Similar results were observed for amino acids. Conclusions: Taken as a whole, the fruits of C. siliquastrum could be described as the best source for most of the identified compounds. The M. germanica samples were rich in mineral contents, with indications that they can supply 26% of the recommended daily intake per 100 g for K, 16% for Mg, 26% for Fe, 63% for Mn, and 89% for B. The leaves of C. maritimum and A. millefolium are also a good source of K and Mn. Interestingly, the sampled leaves of C. maritimum contained a very high amount of B, representing more than three times the reference nutrient value for 100 g of plant material. In conclusion, these underutilized species can be used to diversify the European food systems by enriching our diets with essential nutrients and health-promoting metabolites. Full article
(This article belongs to the Special Issue Metabolomics of Human Nutrition: The Dot of Human Nutrition and the Circle of Soil, Plants, Animals and Microbes in Relation to It, 2nd Edition)
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15 pages, 2863 KB  
Article
Resistant Potato Starch Supplementation Increases the Serum Levels of Choline and Sphingomyelins Without Affecting Trimethylamine Oxide Levels
by Jason R. Bush, Jun Han and David R. Goodlett
Metabolites 2025, 15(10), 662; https://doi.org/10.3390/metabo15100662 - 11 Oct 2025
Cited by 1 | Viewed by 2013
Abstract
Background/Objectives: The prebiotic effect of resistant potato starch (RPS) has been demonstrated, but the role of this nutrient in choline metabolism and the production of microbially modified choline-derived toxins is unknown. Methods: We performed post hoc analysis comparing changes in choline and related [...] Read more.
Background/Objectives: The prebiotic effect of resistant potato starch (RPS) has been demonstrated, but the role of this nutrient in choline metabolism and the production of microbially modified choline-derived toxins is unknown. Methods: We performed post hoc analysis comparing changes in choline and related metabolites in serum from baseline to the week 4 time point in a human clinical trial evaluating daily consumption of 3.5 g RPS versus a placebo. Results: Choline levels increased in the RPS consuming group, while levels of trimethylamine decreased and levels of the cardiovascular toxin trimethylamine oxide were unaffected by RPS consumption. Increases in choline were positively correlated with increases in Akkermansia in the gut. Oxidation of choline to betaine was unaffected by RPS, as was acetylcholine metabolism. Levels of various saturated even acyl chain and hydroxylated acyl chain sphingomyelins were increased in RPS consuming participants, and levels of phospholipid degradation products phosphocholine and glycerophosphocholine were decreased. Conclusions: These data suggest that RPS enhances choline absorption without increasing TMAO and stimulates the incorporation of choline into sphingomyelins containing saturated even acyl chains and hydroxylated acyl chains. Future studies assessing the physiological consequences, such as cognitive or neurological benefits, of enhanced choline absorption and sphingomyelin levels in people consuming RPS are warranted. Full article
(This article belongs to the Special Issue Metabolomics of Human Nutrition: The Dot of Human Nutrition and the Circle of Soil, Plants, Animals and Microbes in Relation to It, 2nd Edition)
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13 pages, 427 KB  
Article
Resistant Potato Starch Supplementation Increases Serum Antioxidant Levels in a Randomized Trial
by Jason R. Bush, Jun Han and David R. Goodlett
Metabolites 2025, 15(10), 661; https://doi.org/10.3390/metabo15100661 - 10 Oct 2025
Cited by 1 | Viewed by 2373
Abstract
Background/Objectives: The prebiotic effect of resistant potato starch (RPS) has been demonstrated, but the antioxidant properties associated with this ingredient have not been explored. Methods: We performed post hoc analysis of serum metabolomic data from a clinical trial evaluating 3.5 g [...] Read more.
Background/Objectives: The prebiotic effect of resistant potato starch (RPS) has been demonstrated, but the antioxidant properties associated with this ingredient have not been explored. Methods: We performed post hoc analysis of serum metabolomic data from a clinical trial evaluating 3.5 g RPS per day consumption (n = 24) versus a placebo (n = 24) for 4 weeks in a randomized clinical trial (NCT05242913). Results: Levels of the exogenous antioxidants all-trans retinol and α-tocopherol increased in the RPS-consuming group. Among endogenous antioxidants, the concentration of coenzyme Q10 (CoQ10) increased in both treatment groups, while uric acid was unaffected. Hippuric acid, a marker of polyphenol metabolism, was unaffected by treatment, as was the abundance of the tryptophan metabolites kynurenine and 3-hydroxyanthranillic acid. However, levels of 3-hydroxykynurenine were decreased in both treatment groups. Levels of the advanced glycation end products NƐ-(1-carboxymethyl)-L-lysine and NƐ-(1-carboxyethyl)-L-lysine, markers of chronically elevated oxidative stress, were unaffected by treatment. Notably, increases in serum all-trans retinol were correlated with increases in Akkermansia. Conclusions: RPS enhances the absorption of antioxidants all-trans retinol and α-tocopherol from the diet and also influences CoQ10 levels and tryptophan metabolism. Future studies assessing the physiological consequences of enhanced antioxidant absorption in people consuming RPS over a longer duration are warranted. Full article
(This article belongs to the Special Issue Metabolomics of Human Nutrition: The Dot of Human Nutrition and the Circle of Soil, Plants, Animals and Microbes in Relation to It, 2nd Edition)
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