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Metabolites
Special Issues
Emerging Applications of Metabolomics in Fermented Food
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Emerging Applications of Metabolomics in Fermented Food

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

Deadline for manuscript submissions: 28 February 2026 | Viewed by 10467

Special Issue Editors

Prof. Dr. Eiichiro Fukusaki

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Guest Editor
Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
Interests: food metabolomics; fermented food; fermentation; fermentation microorganisms; flavor; food secondary function; sensory evaluation; food ternary function; health-promoting function; nutrition
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Akira Oikawa

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Guest Editor
Graduate School of Agriculture, Kyoto University, Kyoto, Japan
Interests: metabolomics; bioorganic chemistry; analytical chemistry; photochemistry; food chemistry; natural products
Dr. Yasuyo Sekiyama

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Guest Editor
Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
Interests: bioorganic chemistry; NMR metabolomics; NMR microscopy; natural product chemistry
Dr. Kazuhiro Iwashita

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Guest Editor
National Research Institute of Brewing, Higashihiroshima, Japan
Interests: brewing; Japanese sake; rice-koji

Special Issue Information

Dear Colleagues,

Metabolomics is a science based on comprehensive metabolite analysis and has recently attracted attention as a method for describing the properties and states of plant, animals and/or microorganisms based on their metabolite profiles. Considering food as a research target, metabolomics is useful for analyzing the performance and function of food itself.

Fermented foods are unique foods that are highly palatable and exhibit complex flavors (secondary functions of foods) and are extremely useful, often having health-promoting functions (tertiary functions of foods). However, the relationships among flavor, tertiary functions, and metabolite profiles of fermented foods are complex and synergistic, and their elucidation is not easy.

For this Special Issue, we welcome submissions presenting metabolomics research results that contribute to the elucidation of the functions of fermented foods.

Specifically, we welcome submissions concerned with the following topics:

1) Metabolomics studies that contribute to the elucidation of the relationship between the flavors of fermented foods and their components;

2) Metabolomics research contributing to the elucidation of health-promoting functions of fermented foods;

3) Research on microorganisms involved in fermented foods;

4) Metabolomics research contributing to the elucidation of the relationship between fermented foods and intestinal microflora.

Prof. Dr. Eiichiro Fukusaki
Prof. Dr. Akira Oikawa
Dr. Yasuyo Sekiyama
Dr. Kazuhiro Iwashita
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 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

  • food metabolomics
  • fermented food
  • fermentation
  • fermentation microorganisms
  • flavor
  • food secondary function
  • sensory evaluation
  • health-promoting function
  • food ternary function
  • nutrition

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Published Papers (4 papers)

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Research

38 pages, 11090 KB  
Article
Impact of Natural Fermentation on Mineral Composition, Resistant and Non-Resistant Starches, Microbial Diversity, and Global Metabolite Profiles in Commercial Poi from Hawai‘i
by Nyan Stillwell, Vedbar S. Khadka and Pratibha V. Nerurkar
Metabolites 2025, 15(11), 748; https://doi.org/10.3390/metabo15110748 - 18 Nov 2025
Viewed by 630
Abstract
Background/Objectives: Taro (Colocasia esculenta L.) is a nutritionally rich and historically significant crop widely consumed in tropical and subtropical regions. Poi, a traditional Hawaiian food made from mashed cooked taro corms, is lauded for its digestibility, prebiotic properties, and potential health benefits. [...] Read more.
Background/Objectives: Taro (Colocasia esculenta L.) is a nutritionally rich and historically significant crop widely consumed in tropical and subtropical regions. Poi, a traditional Hawaiian food made from mashed cooked taro corms, is lauded for its digestibility, prebiotic properties, and potential health benefits. The goal of our study was to evaluate the effects of natural fermentation on the nutritional and metabolic profiles of five commercial poi brands from Hawai‘i. Methods: All poi were fermented at 25 °C for 24 h and 48 h. Resistant starch (RS) and non-resistant starch (NRS) were analyzed using Megazyme assay kits, minerals were analyzed by the EPA 3050B method, fermenting bacteria were analyzed by 16S sequencing, and global metabolites were analyzed using a gas chromatography time-of-flight mass spectrometer. Results: RS and NRS significantly increased in fermented poi, while mineral composition remained unaffected. Untargeted global metabolomic analysis revealed fermentation-induced shifts in metabolite profiles, with increased amino acid concentrations but no changes in essential fatty acids, vitamin E, or flavanols. Fermentation increased the dominance of health-promoting lactic acid bacteria (LAB) such as Leuconostoc, Lactococcus, Weissella, and Lactobacillus, known for their health-promoting properties. No significant correlations were identified among the fermenting bacteria and metabolites. This is probably one of the first comprehensive evaluations to identify the impact of fermentation on the starch, mineral, fermenting microbes, and metabolite content of commercial poi and show the presence of 18 amino acids, including nine essential amino acids. Conclusions: Our findings highlight the nutritional and microbiological significance of fermented poi and its potential as a functional food. Further studies are warranted to explore the health benefits and probiotic effects of poi. Full article
(This article belongs to the Special Issue Emerging Applications of Metabolomics in Fermented Food)
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14 pages, 3096 KB  
Article
Tracking Metabolite Variations during the Degradation of Vegetables in Rice Bran Bed with Intact-State Nuclear Magnetic Resonance Spectroscopy
by Kengo Ito, Ryusei Yamamoto and Yasuyo Sekiyama
Metabolites 2024, 14(7), 391; https://doi.org/10.3390/metabo14070391 - 19 Jul 2024
Cited by 1 | Viewed by 1923
Abstract
Fermentation—a process of compound degradation by microorganisms—is a traditional food processing method utilized worldwide for the long-term preservation of fresh foods. In recent years, fermented foods have gained attention as health foods. Fermentation increases the nutritional value of ingredients, producing complex flavors and [...] Read more.
Fermentation—a process of compound degradation by microorganisms—is a traditional food processing method utilized worldwide for the long-term preservation of fresh foods. In recent years, fermented foods have gained attention as health foods. Fermentation increases the nutritional value of ingredients, producing complex flavors and aromas. To identify unknown components in fermented foods, it is necessary to analyze compounds and conditions nondestructively and comprehensively. We performed intact-state nuclear magnetic resonance (NMR) spectroscopy using intermolecular single quantum coherence (iSQC) to detect the degradation of vegetables directly and nondestructively. We used two types of vegetables and a rice bran bed (nukazuke), which is used for traditional vegetable fermentation in Japan. Major metabolites such as saccharides, organic acids, and amino acids were identified in iSQC-sliced spectra. Comparing NMR signal intensities during degradation revealed the transition of metabolites characteristic of lactic acid fermentation. A pathway-based network analysis showed pathways involved in amino acid metabolism and lactic acid fermentation. Our analytical approach with intact-state NMR spectroscopy using iSQC demonstrated that it may be effective in other experimental systems, allowing for the evaluation of phenomena that have been conventionally overlooked in their true state. Full article
(This article belongs to the Special Issue Emerging Applications of Metabolomics in Fermented Food)
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14 pages, 3930 KB  
Article
Investigation of Rhizopus oligosporus Metabolites in Fermented Wheat Bran and Its Bio Function in Alleviating Colitis in Mice Model
by Afifah Zahra Agista, Yu-Shan Chien, Takuya Koseki, Hazuki Nagaoka, Takuto Ohnuma, Yusuke Ohsaki, Chiu-Li Yeh, Suh-Ching Yang, Ardiansyah, Slamet Budijanto, Michio Komai and Hitoshi Shirakawa
Metabolites 2024, 14(7), 359; https://doi.org/10.3390/metabo14070359 - 26 Jun 2024
Cited by 1 | Viewed by 3969
Abstract
Wheat bran (WB) is a low-value by-product of the wheat milling industry. Solid-state fermentation with Rhizopus oligosporus is performed to improve WB’s nutritional quality (RH). Twenty-five mice (11-week-old C57BL/6N male mice) were divided into three groups. The first group was fed a control [...] Read more.
Wheat bran (WB) is a low-value by-product of the wheat milling industry. Solid-state fermentation with Rhizopus oligosporus is performed to improve WB’s nutritional quality (RH). Twenty-five mice (11-week-old C57BL/6N male mice) were divided into three groups. The first group was fed a control diet (n = 8), the second group a 10% WB-supplemented diet (n = 8), and the last group had a 10% RH-supplemented diet (n = 9). The diet treatment was administered for 4 days before dextran sodium sulfate (DSS, 3% in drinking water) was administered for 9 days. RH supplementation prevented bodyweight loss and reduced the disease activity index in mice. An increase in the level of SCFAs in mouse intestines was detected post-RH supplementation, suggesting that SCFAs might have contributed to its anti-colitis effect. Metabolome analysis was conducted to explore other bioactive compounds in RH. R. oligosporus fermentation significantly increased the amounts of ergothioneine, arginine, branched-chain amino acids, and adenosine in wheat bran. All of these compounds are known to have antioxidant and anti-inflammatory capacities. These bioactive compounds might also have contributed to the RH’s ability to ameliorate DSS-induced colitis. Full article
(This article belongs to the Special Issue Emerging Applications of Metabolomics in Fermented Food)
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15 pages, 4025 KB  
Article
Time-Course Metabolomic Analysis: Production of Betaine Structural Analogs by Fungal Fermentation of Seaweed
by Nao Inoue, Keisuke Tsuge, Teruyoshi Yanagita, Akira Oikawa and Koji Nagao
Metabolites 2024, 14(4), 201; https://doi.org/10.3390/metabo14040201 - 3 Apr 2024
Cited by 6 | Viewed by 2588
Abstract
Betaine structural analogs are compounds characterized by the presence of positive and negative charges in a single molecule and have been reported to have physiological properties, such as anti-inflammatory activities. In this study, we performed a metabolomic analysis of metabolite composition changes during [...] Read more.
Betaine structural analogs are compounds characterized by the presence of positive and negative charges in a single molecule and have been reported to have physiological properties, such as anti-inflammatory activities. In this study, we performed a metabolomic analysis of metabolite composition changes during the fermentation of Neopyropia yezoensis, an edible red alga, with Aspergillus oryzae for 72 h. The results indicated that three specific betaine structural analogs (betaine, stachydrine, and carnitine) exhibited significant changes in production by the end of the 72 h fermentation period. Time-course analysis suggested that betaine was generated from the precursor choline at 12–24 h during the late stage of fungal growth, while stachydrine was generated from the precursor-related compound glutamic acid at 48–72 h during the sporulation stage. However, the contribution of the precursor lysine to the increased production of carnitine during the 12–72 h period was unclear. This study provides useful information on the efficient production of betaine structural analogs by the fungal fermentation of seaweed as well as various other food materials. Full article
(This article belongs to the Special Issue Emerging Applications of Metabolomics in Fermented Food)
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