Advances in Beneficial Food Microorganisms: Isolation, Identification, Characterization and Applications: 2nd Edition

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

Deadline for manuscript submissions: 20 June 2026 | Viewed by 6382

Special Issue Editors


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Guest Editor
School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, China
Interests: acidic functional polysaccharide biosynthesis; aromatic compounds; food fermentation; metabolic engineering; microbiomes
Special Issues, Collections and Topics in MDPI journals

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Guest Editor Assistant
School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
Interests: aromatic compounds; food fermentation; flavor perception

Special Issue Information

Dear Colleagues,

The first volume of this Special Issue (https://www.mdpi.com/journal/foods/special_issues/65A7M6SPG6) was a great success and gained the attention and interest of many scholars. I extend my thanks to all contributors for their work and support. As this topic continues to play a pivotal role in research, we are looking forward to launching the second volume of this Special Issue.

Microorganisms are indispensable in the food industry, e.g., functional food processing, traditional food fermentation, and food enzyme production. At the same time, microorganisms in food or food processing may possess a particular metabolic pathway that synthesizes significant chemical products, expolysaccharides, aromatic compounds, pigments, etc., thereby showing their potential application for the scale-up biosynthesis of these products. In recent years, research on the isolation, identification, characterization, and application of food microorganisms has undergone rapid development and achieved significant progress through the painstaking efforts of researchers. Therefore, this Special Issue aims to provide a broader perspective of the latest advances in beneficial food microorganisms. We intend to address the following questions: (1) Where can we explore new sources of beneficial food microorganisms? (2) How can we isolate these new microorganisms? (3) How can we identify their functional components? (4) How can we illustrate their functional/beneficial component metabolic pathways? (5) How can we implement the application or potential of beneficial food microorganisms in practice? Methodological advances in all areas of beneficial food microorganisms, from fundamental research to applied research, will be covered. We welcome the submission of original research and review articles on topics including, but not limited to, the following:

  • Microbiomes;
  • Metagenomes;
  • Enzyme engineering;
  • Probiotics;
  • Expolysaccharides;
  • Aromatic compounds;
  • Pigments;
  • Vitamins;
  • Biodegradation;
  • Food fermentation.

Dr. Xiaomin Li
Guest Editor

Dr. Ling Zhang
Guest Editor Assistant

Manuscript Submission Information

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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

  • microbiomes
  • metagenomes
  • enzyme engineering
  • probiotics
  • expolysaccharides
  • aromatic compounds
  • pigments
  • vitamins
  • biodegradation
  • food fermentation

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Published Papers (3 papers)

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Research

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16 pages, 5814 KB  
Article
Characterization of Biofilm-Forming Lactic Acid Bacteria from Traditional Fermented Foods and Their Probiotic Potential
by Peilin Yao, Min Kang and Mohd Esah Effarizah
Foods 2025, 14(24), 4299; https://doi.org/10.3390/foods14244299 (registering DOI) - 14 Dec 2025
Abstract
A biofilm is a self-protective material formed by microorganisms to resist adverse environments. As an important group of microorganisms in the food industry and the human intestine, lactic acid bacteria (LAB) demonstrate enhanced probiotic activity in their biofilm state. In this study, a [...] Read more.
A biofilm is a self-protective material formed by microorganisms to resist adverse environments. As an important group of microorganisms in the food industry and the human intestine, lactic acid bacteria (LAB) demonstrate enhanced probiotic activity in their biofilm state. In this study, a total of 90 LAB isolates from various traditional fermented foods across China were evaluated for their biofilm-forming capacity using the crystal violet staining method. Of these, eight isolates showed strong biofilm-forming capacity. These eight isolates were further evaluated for environmental stress responses, including tolerance to high acid and high bile salt concentrations, resistance to simulated gastrointestinal conditions, and adherence to Caco-2 cells. Four isolates with strong resistance to these stresses and adhesion to Caco-2 cells were selected for comparison between their planktonic and biofilm forms. Among these, the two isolates demonstrating the highest biofilm production capacity were AQ-4 and SY1-3, which were isolated from fermented pear juice and apple juice, respectively. Isolate AQ-4 was then identified as Lactiplantibacillus plantarum based on 16S rDNA sequencing. By integrating biofilm-forming capacity with key biological properties, including stress tolerance and epithelial adhesion, this study focuses on L. plantarum AQ-4, which exhibits distinct microstructural differences between planktonic and biofilm states, as revealed by scanning electron microscopy. The findings suggest that L. plantarum AQ-4 could be used to investigate the differential mechanisms in the planktonic and biofilm states and to act as the theoretical basis for the application of LAB biofilms in the food industry. Full article
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21 pages, 19381 KB  
Article
Insights into Microbial and Metabolite Profiles in Traditional Northern Thai Fermented Soybean (Tuanao) Fermentation Through Metagenomics and Metabolomics
by Sivamoke Dissook, Patcharawadee Thongkumkoon, Pitiporn Noisagul, Chanenath Sriaporn, Sirikunlaya Suwannapat, Weeraya Pramoonchakko, Manida Suksawat, Thanaporn Kulthawatsiri, Jutarop Phetcharaburanin, Teera Chewonarin and Jetsada Ruangsuriya
Foods 2025, 14(17), 3070; https://doi.org/10.3390/foods14173070 - 30 Aug 2025
Cited by 1 | Viewed by 3040
Abstract
Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside [...] Read more.
Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside 1H-NMR and UHPLC-ESI-QTOF-MS/MS metabolomics. Bacillus spp. (phylum Bacilliota) quickly supplanted early Enterobacterales and dominated the mature microbiome. The rise of Bacillus coincided with genes for peptide and carbohydrate utilization and with the accumulation of acetate, free amino acids (glutamine, leucine, alanine, valine) and diverse oligopeptides, whereas citrate and glucose-1-phosphate were depleted. This Bacillus-linked metabolic shift indicates that Tuanao is a promising source of probiotics and bioactive compounds. Our study provides the first system-level view of Tuanao fermentation and offers molecular markers to guide starter-culture design and quality control. Full article
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23 pages, 1325 KB  
Systematic Review
Progress in Research on the Mechanism of GABA in Improving Sleep
by Shuyu Li, Yanhui Li, Chunxu Xue, Ying Zhang, Tong Tong, Zijun Ouyang, Dong Liu, Jun Cai and Haiyan Sun
Foods 2025, 14(22), 3856; https://doi.org/10.3390/foods14223856 - 11 Nov 2025
Viewed by 3060
Abstract
Sleep disorders represent a growing global health concern with significant socio-economic impacts. GABA, a natural bioactive compound abundant in various fermented foods, especially probiotic-fermented foods, has garnered increasing attention for its potential to improve sleep quality. This review systematically elucidates the multi-pathway mechanisms [...] Read more.
Sleep disorders represent a growing global health concern with significant socio-economic impacts. GABA, a natural bioactive compound abundant in various fermented foods, especially probiotic-fermented foods, has garnered increasing attention for its potential to improve sleep quality. This review systematically elucidates the multi-pathway mechanisms by which GABA regulates sleep, focusing on (1) indirect modulation of central sleep–wake circuits via the gut–brain axis through vagal nerve, neuroendocrine, and immune pathways; (2) potential entry into the brain by leveraging the dynamic permeability of the blood–brain barrier (BBB) and transporter-mediated active transport; and (3) metabolic conversion into active substances like γ-hydroxybutyrate (GHB), which synergistically optimizes sleep architecture via multiple receptor systems and energy metabolism. Furthermore, we summarize the sleep-promoting effects of GABA-enriched foods observed in animal and clinical studies and discuss emerging applications, including high-GABA-yielding probiotics and personalized nutrition strategies for sleep intervention. This review provides a theoretical basis and innovative directions for the development of GABA-based functional foods and sleep health management. Full article
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