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Brewing Microorganisms in Fermented Foods: Physiological Characteristics, Succession Patterns and...
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Brewing Microorganisms in Fermented Foods: Physiological Characteristics, Succession Patterns and Metabolic Functions

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

Deadline for manuscript submissions: 18 April 2026 | Viewed by 2006

Special Issue Editors

Prof. Dr. Chongde Wu

E-Mail Website
Guest Editor
College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
Interests: fermented foods; microbial community; multi-omics analyses; food microorganism
Special Issues, Collections and Topics in MDPI journals
Dr. Dingkang Wang

E-Mail Website
Guest Editor
Global Health Institute, School of Public Health, Xi’an Jiaotong University, Xi’an 710061, China
Interests: yeast; stress tolerance; physiology; multi-omics
Dr. Guiqiang He

E-Mail Website
Guest Editor
College of Life Sciences and Agri-Forestry, Southwest University of Science and Technology, Mianyang 621010, China
Interests: fermented foods; microbial community; baijiu

Special Issue Information

Dear Colleagues,

Food microbes are the main drivers of food fermentation, responsible for the transformation of raw ingredients into a diverse array of fermented foods and beverages with enhanced sensory attributes, nutritional value, and shelf-life. Recently, high-throughput sequencing has effectively mapped the taxonomic landscape of these ecosystems, and a deeper physiological and metabolic understanding of the key microorganisms is now crucial to decipher the principles governing community assembly and function. This Special Issue, titled “Brewing Microorganisms in Fermented Foods: Physiological Characteristics, Succession Patterns and Metabolic Functions”, seeks to highlight research that moves beyond census-taking to explore the physiology and metabolic activities of individual microbes and their interactions within complex consortia. We aim to compile studies that elucidate how the intrinsic physiological traits of microorganisms (e.g., stress responses, nutrient utilization, communication) dictate their functional output and ultimately shape the dynamic succession of the entire community.

Prof. Dr. Chongde Wu
Dr. Dingkang Wang
Dr. Guiqiang He
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. 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

  • brewing microorganisms
  • fermented food
  • physiological characteristics
  • metabolic function
  • microbial community
  • microbial succession
  • multi-omics

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Published Papers (3 papers)

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18 pages, 10204 KB  
Article
Evolution of Jiang-Flavor Daqu’s Characteristics During Different Storage Stages and Influence on Simulated Brewing Fermentation
by Zihan Chen, Han Wang, Chongchao Wu, Xing Zheng, Guida Zhu, Jing Yu, Qiuxiang Tang and Ping Song
Foods 2026, 15(2), 220; https://doi.org/10.3390/foods15020220 - 8 Jan 2026
Viewed by 221
Abstract
Daqu quality plays a crucial role in the entire fermentation process of Baijiu. There is no empirical evidence for a scientific consensus on the storage period of Jiang-flavor Daqu and its quality evaluation. This study took Jiang-flavor Daqu from a liquor enterprise in [...] Read more.
Daqu quality plays a crucial role in the entire fermentation process of Baijiu. There is no empirical evidence for a scientific consensus on the storage period of Jiang-flavor Daqu and its quality evaluation. This study took Jiang-flavor Daqu from a liquor enterprise in Sichuan Province as the research object. It explored the changes in physicochemical indexes, microbial communities, and volatile flavor substances of the Daqu within 0–180 days of storage. Combined with simulated brewing experiments, it analyzed the effects of different storage periods of Daqu on fermented grain fermentation and the base wine quality and clarified the metabolic differences between Daqu stored for 30 days and 180 days by means of metabolomics. The results showed that the saccharification power and fermentation power of Daqu first increased and then stabilized, reaching 205 mg/g·h and 0.71 g/g·72, respectively, at 180 days. The microbial diversity first increased and then decreased, with Virgibacillus and Oceanobacillus alternately serving as the dominant bacteria. The flavor substances were more abundant within 60 days of storage, while the content of pyrazine compounds was the highest at 180 days. The wine yield of Daqu stored for 30 days was 2.26 times that of Daqu stored for 180 days. The brewing stage had the greatest impact on metabolites, and flavonoid synthesis was the key metabolic pathway. This study provides theoretical support for the scientific storage of Jiang-flavor Daqu and the standardization of its quality. Full article
(This article belongs to the Special Issue Brewing Microorganisms in Fermented Foods: Physiological Characteristics, Succession Patterns and Metabolic Functions)
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20 pages, 18905 KB  
Article
Process Regulation of Microbial-Driven Aldehyde Metabolism in Sauce-Flavor Baijiu Fermentation
by Bo Chen, Wei Cheng, Yiyun Li, Ying Yang, Jixiang Hu, Huibo Luo, Dan Huang, Wenhua Tong and Yadong Zhang
Foods 2026, 15(1), 17; https://doi.org/10.3390/foods15010017 - 21 Dec 2025
Viewed by 511
Abstract
Aldehyde compounds are crucial for the flavor profile of Baijiu; however, their metabolic interplay with microbial communities remains inadequately understood. This study demonstrates that the dynamics of aldehydes during Sauce-Flavor Baijiu (SFB) fermentation are primarily driven by stage-specific microbial activities. Based on microbial [...] Read more.
Aldehyde compounds are crucial for the flavor profile of Baijiu; however, their metabolic interplay with microbial communities remains inadequately understood. This study demonstrates that the dynamics of aldehydes during Sauce-Flavor Baijiu (SFB) fermentation are primarily driven by stage-specific microbial activities. Based on microbial succession patterns, the fermentation process was divided into early (0–7 days) and late (20–30 days) stages. Seven major aldehydes were identified, with furfural being the dominant component, accounting for over 70% of the total aldehyde content. An integrated Environmental–Microbe–Flavor analysis systematically revealed stage-dependent microbial-metabolite interactions. In the early stage, dominant microorganisms such as Fusarium and Apiotrichum scarabaeorum consumed substrates including starch and reducing sugars. Their growth was strongly promoted by increasing ethanol levels and temperature, thereby accelerating aldehyde transformation. As fermentation progressed, moisture emerged as a key regulatory factor, showing a significant negative correlation with Paenibacillus, suggesting that moisture may shape aldehyde metabolism by modulating microbial community structure. Further moisture regulation (51.1–52.7%) applied in the seventh fermentation cycle showed that increased moisture in Zaopei was inversely correlated with aldehyde transformation efficiency (88.3–75.5%). This study elucidates the moisture-mediated regulatory mechanism underlying microbial metabolism and aldehyde conversion, offering novel insights for optimizing the fermentation process of SFB. Full article
(This article belongs to the Special Issue Brewing Microorganisms in Fermented Foods: Physiological Characteristics, Succession Patterns and Metabolic Functions)
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24 pages, 7612 KB  
Article
Insights into Physicochemical Characteristics, Flavor Development, and Microbial Succession During the Natural Fermentation of Sichuan-Style Black Soybean Soy Sauce
by Yutian Xie, Shenglan Liao, Youming Li, Xianbin Wang, Yunhao Lu, Qixu Fu, Qiang He, Yuanlong Chi and Zhenghong Xu
Foods 2025, 14(23), 4049; https://doi.org/10.3390/foods14234049 - 26 Nov 2025
Viewed by 936
Abstract
Sichuan-style black soybean soy sauce is a traditional fermented condiment renowned for its complex and regionally distinctive flavor profile. This study systematically investigated the physicochemical properties, flavor compounds, and microbial succession during six months of natural fermentation to elucidate the mechanisms underlying its [...] Read more.
Sichuan-style black soybean soy sauce is a traditional fermented condiment renowned for its complex and regionally distinctive flavor profile. This study systematically investigated the physicochemical properties, flavor compounds, and microbial succession during six months of natural fermentation to elucidate the mechanisms underlying its unique flavor formation. Results showed that the amino acid nitrogen level increased to a peak of 1.37 g/100 mL before stabilizing at 1.01 g/100 mL, accompanied by a continuous rise in total acidity (0.69–2.75 g/100 mL). A total of 132 volatile compounds were identified, with esters (e.g., hexanoic acid, methyl ester, hexadecanoic acid, and methyl ester), alcohols (e.g., (E)-2-hepten-1-ol and trans-2-undecen-1-ol), and aldehydes (e.g., benzaldehyde and benzeneacetaldehyde) serving as key differentiating components. Nine taste-active (TAV ≥ 1) and 22 odor-active (ROAV ≥ 1) compounds were recognized as major flavor determinants, among which methional (ROAV = 4.77–119.05), 1-octen-3-ol (ROAV = 40.68–149.35), and 4-ethyl-2-methoxyphenol (ROAV = 4.70–36.26) were dominant contributors imparting sauce-like, mushroom-like, and smoky-clove notes, respectively. Microbial succession revealed a transition from Weissella and Aspergillus dominance in the early stage to salt-tolerant Tetragenococcus and aroma-producing yeasts (Kodamaea and Zygosaccharomyces) in later phases. Beyond organic acids and fermentation parameters (e.g., pH and salinity), microbial interactions were identified as critical drivers shaping community assembly and succession. Metabolic pathway analysis revealed a stage-dependent mechanism of flavor formation. During the initial stage (0–2 months), Aspergillus-mediated proteolysis released free amino acids as key taste precursors. In the later stages (3–6 months), Tetragenococcus and aroma-producing yeasts dominated, synthesizing characteristic esters (e.g., benzoic acid and methyl ester, correlated with Tetragenococcus; r = 0.71, p < 0.05), phenolics (e.g., 4-ethyl-2-methoxyphenol, correlated with Wickerhamomyces; r = 0.89, p < 0.05), and sulfur-containing compounds (e.g., methional, correlated with Wickerhamomyces; r = 0.83, p < 0.05). Full article
(This article belongs to the Special Issue Brewing Microorganisms in Fermented Foods: Physiological Characteristics, Succession Patterns and Metabolic Functions)
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