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The Microbial Community and Its Functions in 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 September 2023) | Viewed by 22812

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Prof. Dr. Chongde Wu

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College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
Interests: traditionally fermented foods; microbial community; multi-omics; environmental stresses; microbial physiology
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Fermented foods, with a history as long as human civilization, form an indispensable part of our daily lives. The microbial community during fermentation is considered essential to the development of foods with a unique flavor, texture, and nutritional profile. In recent years, meta-omics tools have offered the opportunity to characterize and trace the succession of the microbial community, which may contribute towards understanding the microbial interactions, metabolic functions, and mechanisms underlying microbial community assembly. As a result, the construction of a synthetic microbial consortia with the desired functions to improve the manufacturing efficiency of fermented foods is being gradually realized.

Therefore, the purpose of this Special Issue is to reveal the dynamics of the microbial community and its metabolic functions in fermented foods. Particular attention will be paid to studies that address new methods applied in microbial community analysis, and the synthetic microbial community involved in the quality formation of fermented foods.

Prof. Dr. Chongde Wu
Guest Editor

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Keywords

fermented foods
microbial community
high-throughput sequencing
metabolic function
meta-omics techniques
synthetic microbial consortia

Published Papers (11 papers)

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Research

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16 pages, 5803 KiB

Open AccessArticle

Exploring the Role of Active Functional Microbiota in Flavor Generation by Integrated Metatranscriptomics and Metabolomics during Niulanshan Baijiu Fermentation

by Yuanyuan Pan, Ying Wang, Wenjun Hao, Sen Zhou, Chengbao Duan, Qiushi Li, Jinwang Wei and Gang Liu

Foods 2023, 12(22), 4140; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12224140 - 15 Nov 2023

Cited by 2 | Viewed by 1088

Abstract

Active functional microbiota for producing volatile flavors is critical to Chinese baijiu fermentation. Microbial communities correlated with the volatile metabolites are generally explored using DNA-based sequencing and metabolic analysis. However, the active functional microbiota related to the volatile flavor compounds is poorly understood. In this study, an integrated metatranscriptomic and metabolomics analysis was employed to unravel the metabolite profiles comprehensively and the contributing active functional microbiota for flavor generation during Niulanshan baijiu fermentation. A total of 395, 83, and 181 compounds were annotated using untargeted metabolomics, including LC-MS, GC-MS, and HS-SPME-GC-MS, respectively. Significant variances were displayed in the composition of compounds among different time-point samples according to the heatmaps and orthogonal partial least-square discriminant analysis. The correlation between the active microbiota and the volatile flavors was analyzed based on the bidirectional orthogonal partial least squares discriminant analysis (O2PLS-DA) model. Six bacterial genera, including Streptococcus, Lactobacillus, Pediococcus, Campylobacter, Yersinia, and Weissella, and five fungal genera of Talaromyces, Aspergillus, Mixia, Rhizophagus, and Gloeophyllum were identified as the active functional microbiota for producing the volatile flavors. In summary, this study revealed the active functional microbial basis of unique flavor formation and provided novel insights into the optimization of Niulanshan baijiu fermentation. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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17 pages, 2853 KiB

Open AccessArticle

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

by Marie Palmnäs-Bédard, Aline de Santa Izabel, Johan Dicksved and Rikard Landberg

Foods 2023, 12(20), 3827; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12203827 - 19 Oct 2023

Cited by 1 | Viewed by 2627

Abstract

Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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16 pages, 4576 KiB

Open AccessArticle

Temperature, Salinity and Garlic Additive Shape the Microbial Community during Traditional Beetroot Fermentation Process

by Justyna Staninska-Pięta, Jakub Czarny, Łukasz Wolko, Paweł Cyplik, Agnieszka Drożdżyńska, Martyna Przybylak, Katarzyna Ratajczak and Agnieszka Piotrowska-Cyplik

Foods 2023, 12(16), 3079; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12163079 - 16 Aug 2023

Cited by 1 | Viewed by 1317

Abstract

Plant-based traditional fermented products are attracting a lot of interest in global markets. An example of them is beetroot leaven, which is valued for its high bioactive compound content. The variety of production recipes and the spontaneous nature of red beet fermentation favor its high diversity. This study aimed to analyze the impact of external factors—temperature, brine salinity, and garlic dose—on the beetroot fermentation and bacterial metapopulation responsible for this process. The research results confirmed the significant influence of the selected and analyzed factors in shaping the leaven physicochemical profile including organic acid profile and betalain content. Analysis of bacterial populations proved the crucial importance of the first 48 h of the fermentation process in establishing a stable metapopulation structure and confirmed that this is a targeted process driven by the effect of the analyzed factors. Lactobacillaceae, Enterobacteriaceae, and Leuconostocaceae were observed to be the core microbiome families of the fermented red beet. Regardless of the impact of the tested factors, the leaven maintained the status of a promising source of probiotic bacteria. The results of this research may be helpful in the development of the regional food sector and in improving the quality and safety of traditionally fermented products such as beetroot leaven. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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15 pages, 2939 KiB

Open AccessArticle

Microbiota Composition during Fermentation of Broomcorn Millet Huangjiu and Their Effects on Flavor Quality

by Ke Wang, Huijun Wu, Jiaxuan Wang and Qing Ren

Foods 2023, 12(14), 2680; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12142680 - 11 Jul 2023

Cited by 1 | Viewed by 1225

Abstract

Broomcorn millet Huangjiu brewing is usually divided into primary fermentation and post-fermentation. Microbial succession is the major factor influencing the development of the typical Huangjiu flavor. Here, we report the changes in flavor substances and microbial community during the primary fermentation of broomcorn millet Huangjiu. Results indicated that a total of 161 volatile flavor compounds were measured during primary fermentation, and estragole was detected for the first time in broomcorn millet Huangjiu. A total of 82 bacteria genera were identified. Pediococcus, Pantoea, and Weissella were the dominant genera. Saccharomyces and Rhizopus were dominant among the 30 fungal genera. Correlation analysis showed that 102 microorganisms were involved in major flavor substance production during primary fermentation, Lactobacillus, Photobacterium, Hyphodontia, Aquicella, Erysipelothrix, Idiomarina, Paraphaeosphaeria, and Sulfuritalea were most associated with flavoring substances. Four bacteria, Lactobacillus (R1), Photobacterium (R2), Idiomarina (R3), and Pediococcus (R4), were isolated and identified from wheat Qu, which were added to wine Qu to prepare four kinds of fortified Qu (QR1, QR2, QR3, QR4). QR1 and QR2 fermentation can enhance the quality of Huangjiu. This work reveals the correlation between microorganisms and volatile flavor compounds and is beneficial for regulating the micro-ecosystem and flavor of the broomcorn millet Huangjiu. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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17 pages, 6986 KiB

Open AccessArticle

Exploring the Successions in Microbial Community and Flavor of Daqu during Fermentation Produced by Different Pressing Patterns

by Ping Huang, Yao Jin, Mingming Liu, Liqun Peng, Guanrong Yang, Zhi Luo, Dongcai Jiang, Jinsong Zhao, Rongqing Zhou and Chongde Wu

Foods 2023, 12(13), 2603; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12132603 - 5 Jul 2023

Cited by 2 | Viewed by 1314

Abstract

Daqu can be divided into artificially pressed daqu (A-Daqu) and mechanically pressed daqu (M-Daqu) based on pressing patterns. Here, we compared the discrepancies in physicochemical properties, volatile metabolites, and microbiota features between A-Daqu and M-Daqu during fermentation and further investigated the factors causing those differences. A-Daqu microbiota was characterized by six genera (e.g., Bacillus and Thermoactinomyces), while five genera (e.g., Bacillus and Thermomyces) dominated in M-Daqu. The flavor compounds analysis revealed that no obvious difference was observed in the type of esters between the two types of daqu, and M-Daqu was enriched with more alcohols. The factors related to differences between the two types of daqu were five genera (e.g., Hyphopichia). The functional prediction of microbial communities revealed that the functional discrepancies between the two types of daqu were mainly related to ethanol metabolism and 2,3-butanediol metabolism. This study provided a theoretical basis for understanding the heterogeneity of daqu due to the different pressing patterns. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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16 pages, 2777 KiB

Open AccessArticle

Fermented Kamut Sprout Extract Decreases Cell Cytotoxicity and Increases the Anti-Oxidant and Anti-Inflammation Effect

by Hosam Ki, Jun-Seok Baek, Hye-Jin Kim Hawkes, Young Soo Kim and Kwang Yeon Hwang

Foods 2023, 12(11), 2107; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12112107 - 24 May 2023

Viewed by 2937

Abstract

Kamut sprouts (KaS) contain several biologically active compounds. In this study, solid-state fermentation using Saccharomyces cerevisiae and Latilactobacillus sakei was used to ferment KaS (fKaS-ex) for 6 days. The fKaS-ex showed a 26.3 mg/g dried weight (dw) and 46.88 mg/g dw of polyphenol and the β-glucan contents, respectively. In the Raw264.7 and HaCaT cell lines, the non-fermented KaS (nfKaS-ex) decreased cell viability from 85.3% to 62.1% at concentrations of 0.63 and 2.5 mg/mL, respectively. Similarly, the fKaS-ex decreased cell viability, but showed more than 100% even at 1.25 and 5.0 mg/mL concentrations, respectively. The anti-inflammatory effect of fKaS-ex also increased. At 600 µg/mL, the fKaS-ex exhibited a significantly higher ability to reduce cytotoxicity by suppressing COX-2 and IL-6 mRNA expressions as well as that for IL-1β mRNA. In summary, fKaS-ex exhibited significantly lower cytotoxicity and increased anti-oxidant and anti-inflammatory properties, indicating that fKaS-ex is beneficial for use in food and other industries. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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12 pages, 1880 KiB

Open AccessArticle

Bacterial Communities Found in Pit-Wall Mud and Factors Driving Their Evolution

by Hao Zhou, Boyang Xu, Shanshan Xu, Suwei Jiang, Dongdong Mu, Xuefeng Wu and Xingjiang Li

Foods 2023, 12(7), 1419; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12071419 - 27 Mar 2023

Cited by 2 | Viewed by 1460

Abstract

Pit-wall mud (PWM) fosters bacterial communities involved in Baijiu production. PWM varies depending on pit age and height. In this study, we explored the bacterial communities in PWM and factors driving their evolution. The abundance and diversity of bacterial communities were low in new PWM (NPWM). In old PWM (OPWM), similar but diverse bacterial communities were observed at different heights. Lactobacillus was the predominant genus in NPWM, and Caproiciproducens, Aminobacterium, Hydrogenispora, Lactobacillus, Petrimonas, Syntrophomonas, and Sedimentibacter were the dominant genera in OPWM. A decrease was noted in the abundance of Lactobacillus, which indicated evolution. Among all the physicochemical properties, pH had the highest degree of interpretation with an R² value of 0.965. pH also exerted the strongest effect on bacterial communities. The path coefficients of pH on bacterial community diversity and abundance were 0.886 and 0.810, respectively. Caproiciproducens and Clostridium sensu stricto 12 metabolized lactic acid, inhibiting the growth of Lactobacillus at a suitable pH, which led to the maturation of PWM. Our findings enrich the literature on the evolution of bacterial communities in PM and the maturation of PM. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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Review

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24 pages, 7941 KiB

Open AccessReview

Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications—A Comprehensive Review

by Juan J. Román-Camacho, Isidoro García-García, Inés M. Santos-Dueñas, Teresa García-Martínez and Juan C. Mauricio

Foods 2023, 12(19), 3705; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12193705 - 9 Oct 2023

Cited by 4 | Viewed by 5281

Abstract

Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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12 pages, 1229 KiB

Open AccessReview

Flavor Formation in Dry-Cured Fish: Regulation by Microbial Communities and Endogenous Enzymes

by Jiayue Liu, Ruijie Mai, Pingru Liu, Siqi Guo, Juan Yang and Weidong Bai

Foods 2023, 12(16), 3020; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12163020 - 11 Aug 2023

Cited by 6 | Viewed by 1361

Abstract

Dried salted fish is a traditional dry-cured fish that is sprinkled with salt before the curing process. With a unique flavor as well as diverse varieties, dry-cured fish is popular among consumers worldwide. The presence of various microbial communities during the curing process leads to numerous metabolic reactions, especially lipid oxidation and protein degradation, which influence the formation of flavor substances. However, during industrial curing, the quality of dry-cured fish is difficult to control, leading to the formation of products with diverse flavors. This review describes the curing process of dried salted fish, the key microorganisms involved in the curing process of typical dried salted fish products at home and abroad, and the correlation between biological metabolism and flavor formation and the underlying mechanism. This review also investigates the prospects of dried salted fish products, proposing methods for the analysis of improved curing processes and the mechanisms of dried salted fish. Through a comprehensive understanding of this review, modern production challenges can be addressed to achieve greater control of microbial growth in the system and improved product safety. In addition to advancing our understanding of the processes by which volatile flavor compounds are formed in conventional dry-cured fish products, we expect that this work will also offer a theoretical framework for enhancing their flavor in food processing. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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17 pages, 2284 KiB

Open AccessReview

Synergistic Fermentation with Functional Microorganisms Improves Safety and Quality of Traditional Chinese Fermented Foods

by Jingya Fan, Guanyi Qu, Datao Wang, Jian Chen, Guocheng Du and Fang Fang

Foods 2023, 12(15), 2892; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12152892 - 29 Jul 2023

Cited by 2 | Viewed by 2372

Abstract

Traditional fermented foods are favored by people around the world for their positive health and taste advantages. Many of the fermented foods, including Chinese traditional fermented foods, are produced through mixed-culture fermentation. Apart from reducing the formation of harmful compounds such as ethyl carbamate (EC) and biogenic amines (BAs) during food fermentation, it is also difficult to precisely control and regulate the fermentation process based on the control of environmental conditions alone, due to the complex microbiota and an unclarified fermentation mechanism. In this review, key microorganisms involved in Chinese fermented foods such as baijiu, soy sauce, and vinegar production are elaborated, and relations between microbial composition and the aroma or quality of food are discussed. This review focuses on the interpretation of functions and roles of beneficial (functional) microorganisms that participate in food fermentation and the discussion of the possibilities of the synergistic use of functional microorganisms to improve the safety and quality of Chinese fermented foods. Conducting work toward the isolation of beneficial microorganisms is a challenge for modern food fermentation technology. Thus, methods for the isolation and mutagenesis of functional microbial strains for synergistic food fermentation are summarized. Finally, the limitations and future prospects of the use of functional microorganisms in traditional Chinese fermented foods are reviewed. This review provides an overview of the applications of synergistic fermentation with functional microorganisms in the improvement of the safety or sensory qualities of fermented foods. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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18 pages, 320 KiB

Open AccessReview

Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods

by Jiaxuan Wang, Shuyue Hao and Qing Ren

Foods 2023, 12(14), 2691; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12142691 - 13 Jul 2023

Cited by 1 | Viewed by 1310

Abstract

Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods. Full article

(This article belongs to the Special Issue The Microbial Community and Its Functions in Fermented Foods)

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