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Food Microorganism Contribution to Fermented Foods

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

Deadline for manuscript submissions: closed (10 February 2026) | Viewed by 20970

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Prof. Dr. Xinping Lin

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Guest Editor

National Marine Food Engineering Technology Research Center, Dalian Polytechnic University, Dalian, China
Interests: animal-based proteins; fermentation; flavor; microorganisms; fermented foods
Special Issues, Collections and Topics in MDPI journals

Dr. Jing Lv

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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

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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 (11 papers)

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Research

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14 pages, 1987 KB

Open AccessArticle

Development of a Novel Chocolate Utilizing Mushroom Fermentation and Associated Changes in Beneficial Components

by Shiori Fukuda, Momoka Nakata, Yuka Sameshima, Naomi Takemoto and Tokumitsu Matsui

Foods 2026, 15(6), 1045; https://doi.org/10.3390/foods15061045 - 16 Mar 2026

Viewed by 583

Abstract

This study investigated the secondary fermentation of cocoa beans using mushrooms to further improve the quality of beans. Cocoa beans were fermented using 42 species of basidiomycetes and ascomycetes. Mycelial growth was observed in 29 strains. When 75% cocoa chocolate was prepared using the cocoa beans in which mycelial growth was observed, theobromine concentration was higher in 17 strains compared with the control. Furthermore, caffeine concentration was similar to or lower than the control in all strains. Chocolate produced using cocoa beans fermented with particularly Polyporus arcularius, Peziza vesiculosa, and Urnula craterium exhibited significantly higher theobromine concentrations. Compared to the control theobromine concentration of 7.53 mg/g, P. arcularius showed 9.25 mg/g, 9.13 mg/g for P. vesiculosa, and 9.05 mg/g for U. craterium. Furthermore, the reducing sugar concentration and total polyphenol concentration increased, and the antioxidant activity was similar to or higher than that of the control. These results suggest that secondary fermentation using mushrooms could be used to develop chocolate characterized by high theobromine, low caffeine, and rich polyphenol content. Full article

(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)

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17 pages, 34428 KB

Open AccessArticle

Genetic Modulation of ATF1 in Saccharomyces cerevisiae for Enhanced Acetate Ester Production and Flavor Profile in a Sour Meat Model System

by Ning Zhao, Ying Yue, Shufeng Yin, Hao Liu, Xiaohan Jia, Ning Wang, Chaofan Ji, Yiwei Dai, Liguo Yin, Huipeng Liang and Xinping Lin

Foods 2026, 15(2), 378; https://doi.org/10.3390/foods15020378 - 21 Jan 2026

Viewed by 522

Abstract

Acetate esters, synthesized by alcohol acyltransferase (AATases) encoded primarily by the ATF1 gene, are pivotal for the desirable fruity aroma in fermented foods. However, the role and regulatory impact of ATF1 in solid-state fermented meat remain largely unexplored. This study engineered Saccharomyces cerevisiae by knocking out and overexpressing ATF1 to investigate its influence on flavor formation in a sour meat model system. Compared to the wild-type strain, ATF1 overexpression (SCpA group) increased ethyl acetate content by 70.15% and uniquely produced significant levels of isoamyl acetate. Conversely, ATF1 deletion (SCdA group) led to a 61.23% reduction in ethyl acetate. Transcriptomic analysis revealed that ATF1 overexpression triggered a systemic metabolic shift, not only activating the final esterification step but also upregulating key genes in central carbon metabolism (SUC2, ICL1), amino acid biosynthesis, and precursor supply pathways (ACS2, ADH1). This synergistic regulation redirected metabolic flux towards the accumulation of both alcohol and acyl-CoA precursors, thereby amplifying acetate ester synthesis. Our findings demonstrate that ATF1 is a critical engineering target for flavor enhancement in fermented meats and uncover a broader metabolic network it influences, providing a robust strategy for the targeted modulation of food flavor profiles. Full article

(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)

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18 pages, 4695 KB

Open AccessArticle

Differences in Nutrition and Sensory Quality Between Cooked Soybeans, Fermented Natto, and Post-Ripening Natto

by Yuguang He, Yuanyuan Jiang, Da Li, Xue Ou, Xinyu Miao, Mubai Sun, Honghong Niu, Mei Hua, Ying Su, Jinghui Wang and Zhuo Liu

Foods 2026, 15(2), 237; https://doi.org/10.3390/foods15020237 - 9 Jan 2026

Viewed by 1397

Abstract

Microbial fermentation is an important means to enhance the nutrition and functionality of food, and soybean fermentation has a long history and a wide variety of products. This study systematically compared the effects of fermentation and post-ripening processes of Bacillus subtilis natto JLCC513 on the nutritional components, active substances, and sensory characteristics of soybeans. The experimental results showed that, in terms of basic nutrition, fermentation led to a significant decrease in fat and reducing sugar content, followed by an initial increase and then a decrease in total protein content. In contrast, water-soluble protein continued to increase, and the total amount of free amino acids surged. The active nutritional indicators before and after soybean fermentation showed that nattokinase activity continued to increase during fermentation and post-ripening. At the same time, the number of viable bacteria decreased slightly during post-ripening. The increase in the proportion of easily absorbed aglycone-type isoflavones before and after soybean fermentation is accompanied by a sustained increase in vitamin K2 and gamma aminobutyric acid (GABA) content. In terms of sensory quality, color-difference analysis shows a decrease in brightness (L value) and an increase in redness (a value), resulting in the characteristic yellow-brown color of natto. In terms of texture characteristics, the hardness decreases, while the viscosity and elasticity are significantly enhanced. Through GC-IMS analysis of volatile aromas during soybean fermentation and post-ripening, it was found that esters (such as ethyl acetate) and pyrazines (such as 2,3-dimethylpyrazine) increased, and the product flavor shifted from grassy to fruity and nutty. In summary, natto bacteria enhance the digestibility, nutritional value, and sensory acceptance of soybeans through enzymatic hydrolysis and metabolic transformation. The post-ripening stage plays a key role in flavor maturation and further accumulation of active ingredients. Full article

(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)

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17 pages, 3225 KB

Open AccessArticle

Screening of Lactic Acid Bacteria and RSM-Based Optimization for Enhancing γ-Aminobutyric Acid (GABA) Accumulation in Orange Juice

by Shufeng Yin, Yiyao Wang, RuiXue Zhao, Ning Zhao, Hao Liu, Yining Tang, Ningbo Qin, Yiwei Dai and Xinping Lin

Foods 2026, 15(1), 71; https://doi.org/10.3390/foods15010071 - 25 Dec 2025

Cited by 2 | Viewed by 935

Abstract

Inoculated fermentation can enhance the flavor, nutrition, and functionality of juice. The lactic acid bacteria (LAB) are commonly used as starter cultures. This study screened LAB for orange juice fermentation and optimized fermentation factors using response surface methodology (RSM) to improve GABA content in orange juice. A total of 52 LAB strains were screened, and Lacticaseibacillus paracasei ZY (Lcb. paracasei ZY) and Lacticaseibacillus rhamnosus SN12 (Lcb. rhamnosus SN12) presented higher GABA yields and adaptability to substrates. The optimized fermentation factors for GABA enhancement in orange juice were as follows: initial pH of 5.5, fermentation temperature of 37 °C, soluble solids content of 12.0 °Bx, inoculum ratio of Lcb. paracasei ZY to Lcb. rhamnosus SN12 as 1:1, inoculum size of 6 Log CFU/mL, and fermentation time of 96 h. Under these optimized conditions, the GABA content reached 0.89 g/L, representing a 39.06% increase compared to uninoculated orange juice. This indicates that RSM-based optimization is conducive to increasing GABA content in orange juice and provides a scientific basis for the development of GABA-enriched functional fermented juices. Full article

(This article belongs to the Special Issue Food Microorganism Contribution to Fermented Foods)

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13 pages, 771 KB

Open AccessArticle

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

Cited by 1 | Viewed by 1485

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 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

Open AccessArticle

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

Cited by 3 | Viewed by 2167

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 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

Open AccessArticle

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

Cited by 1 | Viewed by 1516

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 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

Open AccessArticle

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 1945

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 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

Open AccessArticle

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 2 | Viewed by 2344

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 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

Open AccessArticle

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 7 | Viewed by 1696

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 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

Open AccessReview

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 10 | Viewed by 5362

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, 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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