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Food Microorganism Contribution to Fermented Foods
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Food Microorganism Contribution to Fermented Foods

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

Deadline for manuscript submissions: 10 February 2026 | Viewed by 8533

Special Issue Editors

Prof. Dr. Xinping Lin

E-Mail Website
Guest Editor
National Marine Food Engineering Technology Research Center, Dalian Polytechnic University, Dalian, China
Interests: fermented food; starter culture; flavor; lactic acid bacteria; yeast
Special Issues, Collections and Topics in MDPI journals
Dr. Jing Lv

E-Mail Website
Guest Editor Assistant
Key Laboratory of Cold Chain Food Processing and Safety Control, Henan Province Collaborative Innovation Center of Food Production and Safety, College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, China
Interests: fermented meat product; starter culture; lactic acid bacteria; yeast; flavor

Special Issue Information

Dear Colleagues,

For thousands of years, fermentation has been a cornerstone of food preservation, not only extending the shelf-life of foods and beverages, but also enhancing their nutritional value, health benefits, and disease prevention capabilities. Microorganisms play a crucial role in this process, driving the transformation of raw materials into a variety of beneficial fermented products. This Special Issue aims to explore the extensive contributions of food microorganisms to fermented foods, from traditional practices to innovative biotechnological advancements.

Key areas of focus include studying how microorganisms improve the nutritional composition of foods through fermentation, such as increasing the content of nutrients and bioactive compounds, and the health benefits of fermented foods, including their probiotic effects and disease prevention. The succession and interactions of microorganisms during fermentation, research methods for microorganisms in novel fermented foods, and the development of new starter cultures to meet changing consumer preferences are also crucial. Additionally, we welcome research on both traditional and unconventional food matrices (such as food byproducts) and studies that enhance quality and safety standards through fermentation.

This Special Issue aims to collect original research articles and reviews on cutting-edge approaches to food fermentation. By providing a comprehensive understanding of the role microorganisms play in the fermentation process, we hope to inspire further research and innovation in this vital area of food science.

Prof. Dr. Xinping Lin
Guest Editor

Dr. Jing Lv
Guest Editor Assistant

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

  • food fermentation
  • food microbiology
  • starter cultures
  • lactic acid bacteria
  • yeast
  • probiotic effects
  • bioprocesses
  • functional compounds
  • food safety
  • food quality

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Published Papers (7 papers)

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Research

Jump to: Review

13 pages, 771 KB  
Article
Two-Dimensional GC–ToFMS Analysis of Volatile Organic Compounds in Fermented Camel Milk (Shubat)
by Sagyman Zhadyra, Fei Tao and Ping Xu
Foods 2025, 14(17), 2995; https://doi.org/10.3390/foods14172995 - 27 Aug 2025
Viewed by 688
Abstract
Shubat, a traditional fermented camel milk from Kazakhstan, is renowned for its unique flavor and nutritional properties, though its volatile compound profile remains poorly characterized. In this study, headspace solid-phase microextraction coupled with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (HS-SPME-GC×GC–ToFMS) was employed to [...] Read more.
Shubat, a traditional fermented camel milk from Kazakhstan, is renowned for its unique flavor and nutritional properties, though its volatile compound profile remains poorly characterized. In this study, headspace solid-phase microextraction coupled with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (HS-SPME-GC×GC–ToFMS) was employed to qualitatively identify and semi-quantitatively analyze volatile metabolites in seven Shubat samples collected from four regions of Kazakhstan. Of the 372 volatile organic compounds initially detected, 202 were retained after screening, predominantly comprising esters, acids, alcohols, ketones, and aldehydes. Esters, acids, and alcohol were found to be the most abundant categories. Diversity analyses (α and β) revealed substantial variation across regions, likely influenced by Shubat’s rich and region-specific microbiome. An UpSet analysis demonstrated that 75 volatile compounds were shared among all samples, accounting for over 87% of the total volatile content, indicating a chemically stable core. These findings underscore the chemical complexity of Shubat and provide novel insights into its metabolite composition, thereby establishing a foundation for future sensory, microbial, and quality-related research. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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24 pages, 549 KB  
Article
Evaluation of Nutritional Quality and Oxidation Stability of Fermented Edible Insects
by Anja Vehar, Doris Potočnik, Marjeta Mencin, Mojca Korošec, Blaž Ferjančič, Marta Jagodic Hudobivnik, Polona Jamnik, Ajda Ota, Lenka Kouřimská, Martin Kulma, David John Heath and Nives Ogrinc
Foods 2025, 14(17), 2929; https://doi.org/10.3390/foods14172929 - 22 Aug 2025
Viewed by 791
Abstract
Fermentation, a traditional method for enhancing nutritional value and functionality, has significant potential for improving the quality, safety and acceptability of farmed insect products. In this study, yellow mealworm, house cricket and migratory locust were fermented using Lactobacillus plantarum and a commercial starter [...] Read more.
Fermentation, a traditional method for enhancing nutritional value and functionality, has significant potential for improving the quality, safety and acceptability of farmed insect products. In this study, yellow mealworm, house cricket and migratory locust were fermented using Lactobacillus plantarum and a commercial starter culture for 48 h. Samples were analyzed for proximate composition, amino and fatty acid profiles, elemental composition and oxidation stability. Fermentation reduced total dietary fiber in yellow mealworm (33%) and house cricket (12%), and increased non-protein nitrogen (38% and 16%), while total and protein nitrogen remained unaffected. Fatty acid profiles also remained unchanged, whereas the amino acid composition varied depending on the species and fermentation culture. Essential mineral concentrations varied depending on species and fermentation culture Fe (19–23%), K (25%), Mg (12–23%), Mn (36–378%), Na (20–49%) and P (22%) increased, levels of Se (15%), and Cu (16%) decreased, while Zn levels showed inconsistent trends among treatments. Oxidation stability of yellow mealworm (41–42%) and migratory locust (21–29%) decreased, but improved for house cricket (153–167%). Overall, fermentation enhanced the nutritional value of edible insects, although the extent of improvement varied by species and fermentation culture. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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18 pages, 4809 KB  
Article
Novel Insight into Metabolism Mechanism of Biogenic Amines During Fermentation of Chinese Traditional Fermented Mandarin Fish (Chouguiyu) Based on Metabolism Pathway and Correlation Network
by Jun Li, Daqiao Yang, Yongqiang Zhao, Di Wang, Hui Huang and Chunsheng Li
Foods 2025, 14(16), 2863; https://doi.org/10.3390/foods14162863 - 18 Aug 2025
Viewed by 630
Abstract
A complex microbial community gives the possibility to produce biogenic amines in traditional fermented foods. In this study, the metabolism mechanisms of biogenic amines during fermentation of fermented mandarin fish Chouguiyu were revealed based on the metabolic pathways and correlation analysis. Functional genes [...] Read more.
A complex microbial community gives the possibility to produce biogenic amines in traditional fermented foods. In this study, the metabolism mechanisms of biogenic amines during fermentation of fermented mandarin fish Chouguiyu were revealed based on the metabolic pathways and correlation analysis. Functional genes based on KEGG orthology related to biogenic amine metabolism were selected from the metagenome and were used to construct the biogenic amine metabolic pathways in Chouguiyu. A total of 91 and 75 genera were related to the synthesis and degradation of biogenic amines, respectively. High concentrations of cadaverine and putrescine were observed, while the other biogenic amines were detected in relatively low concentrations. The metabolic mechanisms of various biogenic amines were illuminated by correlation network maps between biogenic amines and microbial synthesis/degradation enzymes. Lactococcus, Flavobacterium, Tessaracoccus, and Yoonia could only degrade and not produce biogenic amines. Acinetobacter and Enterococcus possessed more abundant enzymes for degradation than synthesis. Amine oxidase (K00276), diamine N-acetyltransferase (K00657), and gamma-glutamylputrescine synthase (K09470) were the main biogenic amine degradation enzymes in the microbial community. Lactococcus garvieae, Flavobacterium gelidilacus, Tessaracoccus antarcticus, Yoonia vestfoldensis, Acinetobacter haemolyticus, and Enterococcus ureasiticus were the main microbial species for biogenic amine degradation and could be isolated as the potential strains for biogenic amine degradation in fermented foods. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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17 pages, 1205 KB  
Article
Anti-Obesity and Hepatoprotective Effects of Herring–Saury Oil Fermented by Lactobacillus brevis KCCM13538P in High-Fat-Diet-Induced Mice
by Hyun-Sol Jo, Tae-Won Goo and Sun-Mee Hong
Foods 2025, 14(16), 2862; https://doi.org/10.3390/foods14162862 - 18 Aug 2025
Viewed by 746
Abstract
Background: Obesity-associated liver dysfunction is a key feature of metabolic syndrome. Marine by-products, such as fish oils, offer promising dietary interventions. In this study, we aimed to assess the anti-obesity and hepatoprotective effects of herring–saury by-product-derived fermented fish oil—Gwamegi oil (GmO)—and the same [...] Read more.
Background: Obesity-associated liver dysfunction is a key feature of metabolic syndrome. Marine by-products, such as fish oils, offer promising dietary interventions. In this study, we aimed to assess the anti-obesity and hepatoprotective effects of herring–saury by-product-derived fermented fish oil—Gwamegi oil (GmO)—and the same oil fermented with Lactobacillus brevis KCCM13538P (GmOLb) in a high-fat-diet (HFD)-induced obese mouse model. Methods: GmO was extracted and fermented. Anti-obesity and hepatoprotective effects were assessed using in vitro and in vivo studies. For the in vivo study, female C57BL/6J mice were fed an HFD supplemented with lard (control), GmO, or GmOLb for 60 days. Metabolic and liver function parameters were assessed. Results: In 3T3-L1 adipocytes, GmOLb significantly reduced lipid accumulation and intracellular triglyceride (TG) levels compared with GmO. In HFD-fed mice, GmOLb significantly reduced body weight gain, ovarian fat mass, serum TG, low-density lipoprotein cholesterol, leptin concentration, atherogenic indices, and cardiac risk factor ratio. Furthermore, it reduced liver damage indicators, including alanine aminotransferase, aspartate aminotransferase, and total bilirubin levels. Conclusions: Fermenting herring–saury oil with L. brevis KCCM13538P enhanced its anti-obesity and hepatoprotective effects in HFD-fed mice. GmOLb shows strong potential as a functional dietary lipid for preventing and managing metabolic disorders. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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19 pages, 1406 KB  
Article
Soy Protein Isolate Supplementation Favorably Regulates the Fermentation Characteristics of Debaryomyces hansenii and Flavor Profile in a Sausage Model
by Wenwen Duan, Qiujin Zhu and Jing Wan
Foods 2025, 14(11), 1840; https://doi.org/10.3390/foods14111840 - 22 May 2025
Cited by 1 | Viewed by 1234
Abstract
The metabolic activity of fermentative microorganisms plays a critical role in determining the flavor profile of fermented meat products. Modulating carbon and nitrogen sources represents a promising strategy for enhancing product quality. In this study, Debaryomyces hansenii strains isolated from dry-cured ham were [...] Read more.
The metabolic activity of fermentative microorganisms plays a critical role in determining the flavor profile of fermented meat products. Modulating carbon and nitrogen sources represents a promising strategy for enhancing product quality. In this study, Debaryomyces hansenii strains isolated from dry-cured ham were assessed in a sterile sausage model to evaluate the effects of different carbon sources (sucrose, corn starch) and nitrogen sources (leucine, soy protein isolate) on colony growth, enzyme activity, and physicochemical properties. These nutritional factors significantly affected the fermentation performance of D. hansenii. Corn starch and soy protein isolate increased colony count by 14.94% and 90%, respectively, and enhanced protease activity by 2-fold and 4.5-fold. Both treatments maintained high lipase activity (>50 U/g). Both supplements improved the water-holding capacity and decreased the water activity. Carbon sources reduced the medium pH, whereas nitrogen sources contributed to the maintenance of pH stability. A further analysis indicated that corn starch promoted the accumulation of aldehydes and ketones, which intensified the sourness and suppressed the saltiness. In contrast, soy protein isolate increased the abundance of free amino acids associated with umami and sweetness, and stimulated the formation of esters, ketones, and pyrazines, thereby enhancing flavor richness and umami intensity. Both ingredients also reduced saturated fatty acid levels and increased the unsaturated to saturated fatty acid ratio. Soy protein isolate exhibited a more pronounced effect on D. hansenii fermentation. This study provides a technical reference for enhancing the flavor characteristics of fermented meat products via the adjustment of carbon and nitrogen sources to regulate D. hansenii fermentation. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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18 pages, 3820 KB  
Article
Physicochemical Properties, Antioxidant Activities, and Aromatic Profile of Yogurt Co-Fermented by Weissella cibaria G232 with Traditional Starters
by Qian Huang, Haixiao Ye, Yangyang Yang, Chenglin Zhu and Junni Tang
Foods 2025, 14(9), 1607; https://doi.org/10.3390/foods14091607 - 1 May 2025
Cited by 1 | Viewed by 824
Abstract
To improve the quality and functional properties of yogurts, a multi-starters co-fermentation system was used during yogurt preparation. In this work, Weissella cibaria G232 (added at 0%, 3%, 5%, and 7%) was involved as a co-fermenter with a traditional starter (Lactobacillus delbrueckii [...] Read more.
To improve the quality and functional properties of yogurts, a multi-starters co-fermentation system was used during yogurt preparation. In this work, Weissella cibaria G232 (added at 0%, 3%, 5%, and 7%) was involved as a co-fermenter with a traditional starter (Lactobacillus delbrueckii subsp. bulgaricus G119 and Streptococcus thermophilus Q019). The results showed that W. cibaria G232 co-fermentation could shorten the fermentation time and significantly enhance the viable counts of yogurt (p < 0.05). Moreover, the incorporation of W. cibaria G232 improved the water holding ability, viscosity, and texture of yogurt. Notably, the highest levels of firmness, consistency, and cohesiveness of yogurt were observed at the 5% addition level of W. cibaria G232. Furthermore, co-fermentation with W. cibaria G232 significantly enhanced the antioxidant activity of yogurt, as evidenced by increased free radical scavenging capacity and ferric ion reducing antioxidant power (FRAP) value. The intelligent sensory technology and Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) indicated that co-fermentation with W. cibaria G232 and a traditional starter notably altered the accumulation of aldehydes, ketones, and alcohols in yogurt. These findings suggest that co-fermentation of W. cibaria G232 with a traditional starter present the potential for the quality and functionality improvement of yogurt and also lay the foundation for the application of W. cibaria G232. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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Review

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30 pages, 944 KB  
Review
Biosynthesis of Edible Terpenoids: Hosts and Applications
by Mengyu Wang, Zhengyi Zhang, Xinyu Liu, Zhixuan Liu and Ruirui Liu
Foods 2025, 14(4), 673; https://doi.org/10.3390/foods14040673 - 17 Feb 2025
Cited by 6 | Viewed by 2965
Abstract
Microbial foods include microbial biomass, naturally fermented foods, and heterologously synthesized food ingredients derived from microbial fermentation. Terpenoids, using isoprene as the basic structure, possess various skeletons and functional groups. They exhibit diverse physicochemical properties and physiological activities, such as unique flavor, anti-bacterial, [...] Read more.
Microbial foods include microbial biomass, naturally fermented foods, and heterologously synthesized food ingredients derived from microbial fermentation. Terpenoids, using isoprene as the basic structure, possess various skeletons and functional groups. They exhibit diverse physicochemical properties and physiological activities, such as unique flavor, anti-bacterial, anti-oxidant, anti-cancer, and hypolipemic, making them extensively used in the food industry, such as flavor, fragrance, preservatives, dietary supplements, and medicinal health food. Compared to traditional strategies like direct extraction from natural species and chemical synthesis, microbial cell factories for edible terpenoids have higher titers and yields. They can utilize low-cost raw materials and are easily scaling-up, representing a novel green and sustainable production mode. In this review, we briefly introduce the synthetic pathway of terpenoids and the applications of microbial cell factories producing edible terpenoids. Secondly, we highlight several typical and non-typical microbial chassis in edible terpenoid-producing cell factories. In addition, we reviewed the recent advances of representative terpenoid microbial cell factories with a gram-scale titer in food flavor, food preservation, nutritional enhancers, and medicinal health foods. Finally, we predict the future directions of microbial cell factories for edible terpenoids and their commercialization process. Full article
(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)
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