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Changes in Microbial Community Structure of Fermented Food

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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 (20 February 2026) | Viewed by 5599

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Prof. Dr. Sufang Zhang

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Guest Editor

SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
Interests: fermented food; food microbiology; metabolic engineering; microbial community structure; antioxidants; harmful metabolites during fermentation
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Dr. Yingxi Chen

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School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
Interests: fermented fruit wine; microbial interactions; flavor complexity; antioxidant activity; stress tolerance

Special Issue Information

Dear Colleagues,

Structural changes in the microbial community of fermented foods have a significant impact on various factors, such as flavor profile, nutrient composition, texture, safety, and shelf life. Dynamic changes in the microbial community alter the types and contents of flavour compounds in fermented foods, which in turn affects the flavor characteristics of the final product. Meanwhile, the metabolic activity of microorganisms can synthesize or convert nutrients and affect the nutritional value of fermented foods. In addition, the stability of the microbial community structure plays a key role in the texture, safety, and shelf life of fermented foods, and a rational community structure helps to improve fermentation efficiency and product quality. Therefore, studies in this area are important for optimizing the production process of fermented foods and improving product quality.

Prof. Dr. Sufang Zhang
Dr. Yingxi Chen
Guest Editors

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Keywords

fermented food
food microbiology
microbial community structure
quality
safety
flavor

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Published Papers (4 papers)

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Research

16 pages, 4377 KB

Open AccessArticle

Mechanistic Insights into Levilactobacillus brevis JYX2-Mediated Chinese Sauerkraut Fermentation: Nitrite Degradation and Flavor Enhancement

by Ying Ren, Weihong Tao, Wei Li, Tengda Xue, Zhijie Li, Yiwei Dai and Beiwei Zhu

Foods 2026, 15(3), 485; https://doi.org/10.3390/foods15030485 - 1 Feb 2026

Viewed by 451

Abstract

Traditional Chinese sauerkraut production is hindered by prolonged fermentation times, inconsistent quality, and nitrite accumulation during spontaneous fermentation, which collectively hinder industrial scalability. Levilactobacillus brevis JYX2, isolated from traditional fermented sauerkraut, exhibits excellent acid/salt tolerance, alongside distinctive metabolic pathways (for example, heterolactic fermentation, nitrite degradation, etc.), presenting a viable solution to these challenges. This study assessed its ability to improve sauerkraut quality at laboratory and pilot scales. Results indicated that JYX2 inoculation significantly reduced fermentation duration, expedited pH decline, and elevated total acid levels compared to spontaneous fermentation. The nitrite concentration in the inoculated sauerkraut was 0.72 mg/kg (p < 0.05), significantly lower than 1.86 mg/kg in spontaneous group. At pilot scale, nitrite levels further decreased to 0.44–0.70 mg/kg (p < 0.05), which is below the spontaneous group’s level of 1.61 mg/kg and approaches the “not detected” threshold (<1 mg/kg). Additionally, inoculation increased total organic acids, particularly lactic acid, and enhanced umami/sweet amino acid proportions. Microbial community analysis showed that JYX2-inoculated groups maintained higher relative abundances of core genera, including Leuconostoc and Latilactobacillus, with Firmicutes as the predominant phylum. Pilot tests confirmed consistent JYX2 performance during scale-up, with uniform quality across sauerkraut layers, showing strong industrial adaptability. In conclusion, JYX2 inoculation shortens fermentation, reduces nitrite levels, enhances flavor, and supports standardized, safe, efficient fermented vegetable production. Full article

(This article belongs to the Special Issue Changes in Microbial Community Structure of Fermented Food)

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20 pages, 1825 KB

Open AccessArticle

Lacticaseibacillus rhamnosus WH.FH-19: Probiotic Traits, Fermentation Performance, and Potential for Functional Fermented Milk Production

by Shiyuan Sun, Lu Feng, Liping Sun, Xuemei Zhu, Mo Zhou, Xinling Li and Guangqing Mu

Foods 2026, 15(2), 271; https://doi.org/10.3390/foods15020271 - 12 Jan 2026

Viewed by 594

Abstract

Lacticaseibacillus rhamnosus WH.FH-19 exhibits robust probiotic and technological traits for fermented dairy applications. L. rhamnosus WH.FH-19 shows superior functional potential compared to the benchmark strain Lacticaseibacillus rhamnosus GG. Kinetic studies confirm L. rhamnosus WH.FH-19’s vigorous growth and rapid acidification kinetics in bovine milk. In vitro characterization reveals enhanced probiotic properties, including significantly greater epithelial adhesion, tolerance to gastrointestinal stresses, cholesterol assimilation capacity, and antioxidant activity. Comprehensive safety assessment demonstrated the absence of hemolysis, sensitivity to clinically relevant antibiotics, and negligible tyramine production. Optimal synergistic fermentation with L. bulgaricus CICC 6047 and S. thermophilus CICC 6038 was achieved using a defined inoculum ratio. Under these conditions, L. rhamnosus WH.FH-19 specifically potentiated the activity of the S. thermophilus strain, accelerating fermentation kinetics without subsequent post-acidification while improving product sensory attributes. These findings establish L. rhamnosus WH.FH-19 as a safe, functionally robust probiotic with significant technological benefit for commercial fermented dairy production. Full article

(This article belongs to the Special Issue Changes in Microbial Community Structure of Fermented Food)

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21 pages, 862 KB

Open AccessEditor’s ChoiceArticle

Polyphasic Characterisation of Microbiota Associated with Sant’Agostino Table Olives Flavoured with Foeniculum vulgare

by Antonio Alfonzo, Raimondo Gaglio, Davide Alongi, Elena Franciosi, Giulio Perricone, Giuliana Garofalo, Rosario Prestianni, Vincenzo Naselli, Antonino Pirrone, Nicola Francesca, Giancarlo Moschetti and Luca Settanni

Foods 2025, 14(21), 3689; https://doi.org/10.3390/foods14213689 - 29 Oct 2025

Cited by 1 | Viewed by 1171

Abstract

Sant’Agostino green table olives, traditionally processed in Apulia and flavoured with Foeniculum vulgare, represent a niche product whose microbial ecology remains largely unexplored. This study aimed to characterise the microbiota of the final product (both brine and fruit) after six months of storage with wild fennel. Four production batches were analysed using a combined culture-dependent and culture-independent approach. Microbiological counts revealed variable levels of aerobic mesophilic microorganisms, yeasts, lactic acid bacteria (LAB), and staphylococci, with yeasts and LAB being predominant. Ten LAB strains were identified, including Enterococcus faecium, Leuconostoc mesenteroides subsp. jonggajibkimchii, Leuconostoc mesenteroides subsp. cremoris, Leuconostoc pseudomesenteroides, Lactiplantibacillus plantarum, and Lactiplantibacillus pentosus. Yeast isolates belonged to Candida tropicalis, Torulaspora delbrueckii, and Saccharomyces cerevisiae. Amplicon sequencing (MiSeq Illumina) revealed distinct bacterial profiles between fruit and brine samples, with taxa from Actinobacteria, Bacteroidetes, Enterococcus, Lactobacillus, Leuconostoc, Alphaproteobacteria, Enterobacteriaceae, and other Gammaproteobacteria. Enterococcus and Leuconostoc were consistently detected, while Lactobacillus sensu lato appeared only in one fruit and one brine sample. These findings provide new insights into the microbial diversity of Sant’Agostino olives and contribute to the understanding of their fermentation ecology and potential for quality and safety enhancement. Full article

(This article belongs to the Special Issue Changes in Microbial Community Structure of Fermented Food)

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16 pages, 10801 KB

Open AccessArticle

The Antioxidant Capacity and Flavor Diversity of Strawberry Wine Are Improved Through Fermentation with the Indigenous Non-Saccharomyces Yeasts Hanseniaspora uvarum and Kurtzmaniella quercitrusa

by Ruipeng Wang, Bo Yang, Saihong Jia, Yiwei Dai, Xinping Lin, Chaofan Ji and Yingxi Chen

Foods 2025, 14(5), 886; https://doi.org/10.3390/foods14050886 - 5 Mar 2025

Cited by 10 | Viewed by 2784

Abstract

The production of strawberry wine is an effective strategy for addressing the significant economic losses caused by strawberry spoilage. In recent years, there has been an increase in consumer demand for quality and flavor diversity in fruit wines. Therefore, it is necessary to develop novel strawberry wine products. In this research, we assessed and analyzed the influences of fermentation with Hanseniaspora uvarum, Kurtzmaniella quercitrusa, and Saccharomyces cerevisiae under four fermentation conditions on the fermentation kinetics, organoleptic characteristics, chemical compositions, antioxidant capacities, and flavor profiles of strawberry wines. Strawberry wines fermented with the indigenous non-Saccharomyces yeasts H. uvarum and K. quercitrusa showed higher 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-Azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) free-radical-scavenging capacities and significantly different flavor profiles compared to strawberry wines fermented with S. cerevisiae. In addition, adjusting the initial soluble solids contents of strawberry juices and fermentation temperatures positively affected the quality and flavor profiles of strawberry wines fermented with the H. uvarum and K. quercitrusa strains. Under the condition of 18 °C–20 °Brix, strawberry wine fermented with K. quercitrusa presented the highest antioxidant capacity, with enhanced flavor diversity and color intensity. It is worth noting that K. quercitrusa can be an alternative yeast for producing high-quality strawberry wine with a distinct floral aroma. Full article

(This article belongs to the Special Issue Changes in Microbial Community Structure of Fermented Food)

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