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

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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 (18 April 2026) | Viewed by 5861

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Special Issue Editors

Prof. Dr. Chongde Wu

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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

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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

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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 (7 papers)

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Research

16 pages, 10212 KB

Open AccessArticle

Construction of Synthetic Microbial Community with Core Microorganisms for Soy Sauce Fermentation

by Pengfei Chen, Guocheng Du, Jian Chen and Fang Fang

Foods 2026, 15(10), 1736; https://doi.org/10.3390/foods15101736 - 14 May 2026

Viewed by 188

Abstract

Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce. 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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22 pages, 3343 KB

Open AccessArticle

Surfactin-Producing Bacillus velezensis A1 Inhibits Lactic Acid Bacteria in Jiang-Flavor Baijiu Fermentation

by Xinyue Li, Menglin She, Lingfeng Yi, Guanyu Zhou, Yafei Lian, Chong Yang, Yaokang Wu, Yanfeng Liu, Ying Han and Jianghua Li

Foods 2026, 15(7), 1140; https://doi.org/10.3390/foods15071140 - 26 Mar 2026

Viewed by 637

Abstract

Lactic Acid Bacteria contribute to heightened acidity in the fermentation process of Jiang-flavor Baijiu due to their production of lactic acid. High-temperature Daqu may act as a reservoir for beneficial microorganisms and antimicrobial compounds. In this study, we utilized 16S rRNA and ITS amplicon sequencing to identify microbial taxa in high-temperature Daqu that inhibit the primary lactic acid bacterium involved in Jiang-flavor Baijiu fermentation, Acetilactobacillus jinshanensis, followed by the selection of antagonistic strains. The strain exhibiting the strongest antagonistic activity was identified as Bacillus velezensis based on whole-genome sequencing. Genome analysis revealed 12 secondary metabolite biosynthetic gene clusters, from which one lipopeptide was identified. This lipopeptide was demonstrated to antagonize A. jinshanensis AJS1 by disrupting the cell membrane and inducing leakage of intracellular contents. Collectively, strain A1 and its secondary metabolites exhibit considerable promise as antagonistic agents to mitigate acidity increases triggered by A. jinshanensis AJS1 during the fermentation of Jiang-flavor Baijiu. 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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17 pages, 2558 KB

Open AccessArticle

Elucidating the Impact of High-Temperature Daqu on Base Baijiu of Sauce-Flavor Baijiu: From Key Aroma Compounds to Microbial Origins

by Peng Chen, Shiming Shen, Liangcai Lin, Qijing Liu, Cuiying Zhang and Cheng Zhong

Foods 2026, 15(7), 1124; https://doi.org/10.3390/foods15071124 - 24 Mar 2026

Viewed by 423

Abstract

Jiaomian base baijiu is an important seasoning liquor used in the blending of sauce-flavor baijiu, yet the mechanism underlying its flavor formation remains insufficiently understood. Moreover, the specific contribution of high-temperature Daqu (HTDQ) to the flavor profile of Jiaomian base baijiu has not been clearly defined. Therefore, this study compared the aroma profiles and flavor compounds of Jiaomian and Chuntian base baijiu. Jiaomian base baijiu displayed stronger Qu-aroma and floral–fruity notes, with six differential flavor markers (VIP > 1) identified, including ethyl acetate, acetaldehyde, and n-propanol. Further analysis showed that yellow HTDQ exhibited greater inner–outer heterogeneity in aroma and flavor profiles than white and black HTDQ. It also contained the highest concentration of flavor compounds and exerted the strongest influence on the flavor of Jiaomian base baijiu. By comparing the flavor compounds of HTDQ and base baijiu, 14 key compounds were identified that mediate the influence of HTDQ on the flavor of Jiaomian base baijiu. These compounds were primarily formed during the early to middle stages of HTDQ fermentation. Correlation analysis further indicated that microorganisms during HTDQ fermentation were predominantly positively correlated with the key flavor compounds. Among them, Thermoactinomyces, Byssochlamys, Kazachstania, Leiothecium, and Trichothecium showed the closest associations—positively correlated with compounds such as 1-nonanol and furfuryl alcohol, and negatively correlated with isovaleric acid. Finally, KEGG enrichment analysis of the flavor compounds suggested that Beta Oxidation of Very Long-Chain Fatty Acids, Mitochondrial Beta-Oxidation of Short-Chain Saturated Fatty Acids, and Fatty Acid Biosynthesis are key pathways involved in the formation of these flavor substances. In summary, this study clarifies the key flavor compounds through which different HTDQ types influence base baijiu flavor, reveals the microbial origins and metabolic pathways of these key flavor compounds, and provides a theoretical basis for regulating HTDQ production and improving the quality of base baijiu. 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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18 pages, 4771 KB

Open AccessArticle

Revealing the Functional Microbiota of Caproic Acid-Producing and Lactic Acid-Utilizing Bacteria in the Pit Muds for Chinese Nong-Xiang Baijiu Fermentation

by Qingwei Feng, Xiaohan Li, Lijuan Gong, Yanxia Wei, Zhongxue Bai, Jian Zhou, Yi Ma and Guiqiang He

Foods 2026, 15(3), 416; https://doi.org/10.3390/foods15030416 - 23 Jan 2026

Viewed by 534

Abstract

Low ethyl caproate and high ethyl lactate contents pose a significant challenge in producing Chinese nong-xiang baijiu. The formation of these esters depends on the metabolism of their precursors—caproic acid and lactic acid—within the pit mud (PM) microbiome. However, the specific taxa driving the metabolic flux from lactate accumulation to caproate synthesis remain unclear. This study aimed to identify potential functional microbes capable of caproate biosynthesis and lactate utilization by systematically analyzing PM samples from the upper, middle, and lower layers of three different pit ages (0, 20, and 50 years). Results showed that 50-year-old PM exhibited significantly higher caproic acid and ammonium nitrogen levels, but lower lactic acid content, compared to the 0- and 20-year-old counterparts. Notably, Petrimonas, Caproiciproducens, and Sedimentibacter were significantly enriched in the 50-year-old PM. Their relative abundances correlated positively with caproic acid and negatively with lactic acid. Furthermore, PICRUSt2 analysis indicated higher abundances of genes associated with caproate synthesis and lactate utilization in the 50-year-old microenvironment. We propose that Petrimonas, Caproiciproducens, and Sedimentibacter are potential functional candidates for lactate degradation and caproate generation. These findings provide a scientific basis for modulating the microbiome for “increasing ethyl caproate and reducing ethyl lactate”, thereby enhancing baijiu 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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18 pages, 10204 KB

Open AccessArticle

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 752

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 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

Open AccessArticle

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

Cited by 2 | Viewed by 927

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 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

Open AccessArticle

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

Cited by 3 | Viewed by 1761

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 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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