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Molecular Methods in Food Quality and Microbiological Safety
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Molecular Methods in Food Quality and Microbiological Safety

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

Deadline for manuscript submissions: closed (11 September 2023) | Viewed by 23381

Special Issue Editors

Dr. Youqiang Xu

E-Mail Website
Guest Editor
School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
Interests: food microbiology; molecular methods; fermented food; flavor
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yu Zheng

E-Mail Website
Guest Editor
College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300453, China
Interests: Chinese cereal vinegar; microbial metabolism; bioaugmentation; solid-state fermentation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms serve as an important tool in food processing. For example, the community and metabolism of microorganisms in fermented foods are closely related to the product quality. Meanwhile, the effect of microorganisms on food processing shows duality. Microbial contamination is one of the severe challenges in food processing. How to accurately reveal microbial functions in food processing and detect food pathogens is therefore an important issue in food processing. The development of molecular methods provides important tools for detecting food pathogens or revealing the dynamic changing and possible metabolic mechanisms of microorganisms in food processing. For example, omics technologies (e.g., genomics, transcriptomics and metabolomics) provide useful tools for analyzing the correlation between microbial metabolism and flavor formation in complex microbial fermentation eco-systems. The development of specific molecular detection technologies, such as nucleic acid detection methods, offers a fast and convenient way for detecting target microorganisms in food processing. This Special Issue mainly includes recent studies on the molecular mechanisms of the microbial transformation of raw materials and the generation of flavor substances in food processing, and new methods or technologies for accurately detecting specific microorganisms in the food processing context. The goal is to provide a reference for revealing the effects of microorganisms in food processing on product quality and safety.

Dr. Youqiang Xu
Prof. Dr. Yu Zheng
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • high-throughput sequencing
  • genomics
  • transcriptomics
  • metabolomics
  • microbiology
  • flavor and food quality
  • fermented food
  • food pathogens
  • manufacturing processes
  • metabolic mechanism

Published Papers (9 papers)

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Research

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21 pages, 4117 KiB  
Article
The Production of Intensified Qu and Its Microbial Communities and Aroma Variation during the Fermentation of Huangjiu (Chinese Rice Wine)
by Siman Zheng, Wendi Zhang, Qing Ren, Jihong Wu, Jinglin Zhang, Bowen Wang, Nan Meng, Jinchen Li and Mingquan Huang
Foods 2023, 12(14), 2674; https://doi.org/10.3390/foods12142674 - 11 Jul 2023
Viewed by 889
Abstract
In recent years, intensified Qu (IQ) has been gradually applied to brewing in order to improve the aroma of Huangjiu (Chinese rice wine). In this study, Saccharomyces cerevisiae and Wickerhamomyces anomalus solutions were added to Fengmi Qu (FMQ) from Fangxian, China to produce [...] Read more.
In recent years, intensified Qu (IQ) has been gradually applied to brewing in order to improve the aroma of Huangjiu (Chinese rice wine). In this study, Saccharomyces cerevisiae and Wickerhamomyces anomalus solutions were added to Fengmi Qu (FMQ) from Fangxian, China to produce IQ, and brewing trial was conducted. High-throughput sequencing (HTS) was used to analyze the microbial community in fermentation broth of IQ (IQFB). Headspace solid-phase microextraction (HS-SPME) combined with gas chromatography–mass spectrometry (GC-MS) and sensory evaluation were performed to analyze volatile aroma compounds (VACs) in sample without Qu and both fermentation broths. The results showed that Pediococcus, Cronobacter, Enterococcus, Weissella, and Acinetobacter and Saccharomycopsis, Wickerhamomyces, and Saccharomyces were dominant bacterial and fungal groups, respectively. A total of 115 VACs were detected, and the content of esters including ethyl acetate, isoamyl acetate, and so on was noticeably higher in IQFB. The finding of sensory evaluation reflected that adding pure yeast to Qu could enhance fruit and floral aromas. Correlation analysis yielded 858 correlations between significant microorganisms and different VACs. In addition, prediction of microbial community functions in IQFB revealed global and overview maps and carbohydrate metabolism to be the main one. This study is advantageous for further regulation of the fermentation process of Huangjiu by microbial means. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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16 pages, 3141 KiB  
Article
Effects of the Marinating Process on the Quality Characteristics and Bacterial Community of Leisure Dried Tofu
by Tao Wu, Zhanrui Huang, Liangzhong Zhao, Xiaohu Zhou, Hao Chen, Xiaojie Zhou, Ming Li, Jinsong Zhou and Yingyi Lin
Foods 2023, 12(4), 841; https://doi.org/10.3390/foods12040841 - 16 Feb 2023
Cited by 1 | Viewed by 1361
Abstract
Leisure dried tofu (LD-tofu) was prepared using two different marinating processes: the repeated heating method (RHM) and the vacuum pulse method (VPM). The quality characteristics and bacterial community succession of LD-tofu and the marinade were evaluated. The results showed that the nutrients in [...] Read more.
Leisure dried tofu (LD-tofu) was prepared using two different marinating processes: the repeated heating method (RHM) and the vacuum pulse method (VPM). The quality characteristics and bacterial community succession of LD-tofu and the marinade were evaluated. The results showed that the nutrients in LD-tofu were easily dissolved into the marinade during the marinating process, while the protein and moisture content of RHM LD-tofu changed most dramatically. With the increase in marinade recycling times, the springiness, chewiness and hardness of VPM LD-tofu increased significantly. The total viable count (TVC) of the VPM LD-tofu decreased from the initial value of 4.41 lg cfu/g to 2.51–2.67 lg cfu/g as a result of the marinating process, which had a significant inhibitory effect. Additionally, 26, 167 and 356 communities in the LD-tofu and marinade were detected at the phylum, family and genus levels, respectively. Pearson correlation analysis showed that Pseudomonadaceae, Thermaceae and Lactobacillaceae were closely related to the quality characteristics of LD-tofu, whereas Caulobacteriaceae, Bacillaceae and Enterobacteriae were closely related to the marinade. The present work provides a theoretical basis for the screening of functional strains and quality control in LD-tofu and marinade. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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21 pages, 18025 KiB  
Article
Simulated Fermentation of Strong-Flavor Baijiu through Functional Microbial Combination to Realize the Stable Synthesis of Important Flavor Chemicals
by Youqiang Xu, Mengqin Wu, Dong Zhao, Jia Zheng, Mengqi Dai, Xiuting Li, Weiwei Li, Chengnan Zhang and Baoguo Sun
Foods 2023, 12(3), 644; https://doi.org/10.3390/foods12030644 - 02 Feb 2023
Cited by 22 | Viewed by 2689
Abstract
The solid-state fermentation of Baijiu is complicated by the co-fermentation of many microorganisms. The instability of the composition and abundance of the microorganisms in the fermentation process leads to fluctuations of product quality, which is one of the bottleneck problems faced by the [...] Read more.
The solid-state fermentation of Baijiu is complicated by the co-fermentation of many microorganisms. The instability of the composition and abundance of the microorganisms in the fermentation process leads to fluctuations of product quality, which is one of the bottleneck problems faced by the Strong-flavor Baijiu industry. In this study, we established a combination of functional microorganisms for the stable fermentation of the main flavor compounds of Baijiu, including medium and long-chain fatty acid ethyl esters such as hexanoic acid, ethyl ester; butanoic acid, ethyl ester; octanoic acid, ethyl ester; acetic acid, ethyl ester; 9,12-octadecadienoic acid, ethyl ester; and decanoic acid, ethyl ester in the fermented grains. Our study investigated the effects of microbial combinations on the fermentation from three aspects: microbial composition, microbial interactions, and microbial association with flavor compounds. The results showed that the added functional microorganisms (Lactobacillus, Clostridium, Caproiciproducens, Saccharomyces, and Aspergillus) became the dominant species in the fermentation system and formed positive interactions with other microorganisms, while the negative interactions between microorganisms were significantly reduced in the fermentation systems that contained both Daqu and functional microorganisms. The redundancy analysis showed that the functional microorganisms (Lactobacillus, Saccharomyces, Clostridium, Cloacibacterium, Chaenothecopsis, Anaerosporobacter, and Sporolactobacillus) showed strong positive correlations with the main flavor compounds (hexanoic acid, ethyl ester; lactic acid, ethyl ester; butanoic acid, ethyl ester; acetic acid, ethyl ester; and octanoic acid, ethyl ester). These results indicated that it was feasible to produce Baijiu with a functional microbial combination, and that this could promote stable Baijiu production. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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21 pages, 10903 KiB  
Article
Characteristics and Correlation of the Microbial Communities and Flavor Compounds during the First Three Rounds of Fermentation in Chinese Sauce-Flavor Baijiu
by Youqiang Xu, Mengqin Wu, Jialiang Niu, Mengwei Lin, Hua Zhu, Kun Wang, Xiuting Li and Baoguo Sun
Foods 2023, 12(1), 207; https://doi.org/10.3390/foods12010207 - 03 Jan 2023
Cited by 19 | Viewed by 2894
Abstract
Sauce-flavor Baijiu is representative of solid-state fermented Baijiu. It is significant to deeply reveal the dynamic changes of microorganisms in the manufacturing process and their impact on the formation of flavor chemicals correlated with the quality of Baijiu. Sauce-flavor Baijiu manufacturing process can [...] Read more.
Sauce-flavor Baijiu is representative of solid-state fermented Baijiu. It is significant to deeply reveal the dynamic changes of microorganisms in the manufacturing process and their impact on the formation of flavor chemicals correlated with the quality of Baijiu. Sauce-flavor Baijiu manufacturing process can be divided into seven rounds, from which seven kinds of base Baijius are produced. The quality of base Baijiu in the third round is significantly better than that in the first and second rounds, but the mystery behind the phenomenon has not yet been revealed. Based on high-throughput sequencing and flavor analysis of fermented grains, and correlation analysis, the concentrations of flavor chemicals in the third round of fermented grains were enhanced, including esters hexanoic acid, ethyl ester; octanoic acid, ethyl ester; decanoic acid, ethyl ester; dodecanoic acid, ethyl ester; phenylacetic acid, ethyl ester; 3-(methylthio)-propionic acid ethyl ester; acetic acid, phenylethyl ester; hexanoic acid, butyl ester, and other flavor chemicals closely related to the flavor of sauce-flavor Baijiu, such as tetramethylpyrazine. The changes in flavor chemicals should be an important reason for the quality improvement of the third round of base Baijiu. Correlation analysis showed that ester synthesis was promoted by the bacteria genus Lactobacillus and many low abundances of fungal genera, and these low abundances of fungal genera also had important contributions to the production of tetramethylpyrazine. Meanwhile, the degrading metabolic pathway of tetramethylpyrazine was investigated, and the possible microorganisms were correlated. These results clarified the base Baijiu quality improvement of the third round and helped to provide a theoretical basis for improving base Baijiu quality. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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19 pages, 3076 KiB  
Article
Comparative Transcriptomic and Metabolomic Analyses Reveal the Regulatory Effect and Mechanism of Tea Extracts on the Biosynthesis of Monascus Pigments
by Wen-Long Li, Jia-Li Hong, Jin-Qiang Lu, Shan-Gong Tong, Li Ni, Bin Liu and Xu-Cong Lv
Foods 2022, 11(20), 3159; https://doi.org/10.3390/foods11203159 - 11 Oct 2022
Cited by 3 | Viewed by 1503
Abstract
Monascus pigments (MPs) are natural edible pigments with high safety and strong function, which have been widely used in food and health products. In this study, different types of tea extracts (rich in polyphenols) were used to regulate the biosynthesis of MPs. The [...] Read more.
Monascus pigments (MPs) are natural edible pigments with high safety and strong function, which have been widely used in food and health products. In this study, different types of tea extracts (rich in polyphenols) were used to regulate the biosynthesis of MPs. The results showed that 15% ethanol extract of pu-erh tea (T11) could significantly increase MPs production in liquid fermentation of Monaco’s purpureus M3. Comparative transcriptomic and metabolomic analyses combined with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were used to further explore the regulatory mechanism of T11 on the biosynthesis of MPs. Comparative transcriptomic analysis showed that there were 1503 differentially expressed genes (DEGs) between the Con group and the T11 group, which were mainly distributed in carbohydrate metabolism, amino acid metabolism, energy metabolism, lipid metabolism, metabolism of terpenoids and polyketides, etc. A total of 115 differential metabolites (DMs) identified by metabolomics between the Con and T11 groups were mainly enriched in glutathione metabolism, starch and sucrose metabolism, alanine, aspartic acid and glutamate metabolism and glycine, serine and threonine metabolism, etc. The results of metabolomics were basically consistent with those of gene transcriptomics, indicating that the regulatory effect of T11 on the biosynthesis of MPs is mainly achieved through affecting the primary metabolic pathway, providing sufficient energy and more biosynthetic precursors for secondary metabolism. In this study, tea extracts with low economic value and easy access were used as promoters of MPs biosynthesis, which may be conducive to the application of MPs in large-scale industrial production. At the same time, a more systematic understanding of the molecular regulatory mechanism of Monascus metabolism was obtained through multi-omics analysis. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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11 pages, 17112 KiB  
Article
Microbial Properties of Raw Milk throughout the Year and Their Relationships to Quality Parameters
by Huizhi Yuan, Sufang Han, Shufei Zhang, Yuling Xue, Yaoguang Zhang, Han Lu and Shijie Wang
Foods 2022, 11(19), 3077; https://doi.org/10.3390/foods11193077 - 04 Oct 2022
Cited by 11 | Viewed by 4154
Abstract
Raw milk microbiota is complex and influenced by many factors that facilitate the introduction of undesirable microorganisms. Milk microbiota is closely related to the safety and quality of dairy products, and it is therefore critical to characterize the variation in the microbial composition [...] Read more.
Raw milk microbiota is complex and influenced by many factors that facilitate the introduction of undesirable microorganisms. Milk microbiota is closely related to the safety and quality of dairy products, and it is therefore critical to characterize the variation in the microbial composition of raw milk. In this cross-sectional study, the variation in raw milk microbiota throughout the year (n = 142) from three farms in China was analyzed using 16S rRNA amplicon sequencing, including α and β diversity, microbial composition, and the relationship between microbiota and milk quality parameters. This aimed to characterize the contamination risk of raw milk throughout the year and the changes in quality parameters caused by contamination. Collection month had a significant effect on microbial composition; microbial diversity was higher in raw milk collected in May and June, while milk collected in October and December had the lowest microbial diversity. Microbiota composition differed significantly between milk collected in January–June, July–August, and September–December (p < 0.05). Bacterial communities represented in raw milk at the phylum level mainly included Proteobacteria, Firmicutes and Bacteroidota; Pseudomonas, Acinetobacter, Streptococcus and Lactobacillus were the most common genera. Redundancy analysis (RDA) found strong correlations between microbial distribution and titratable acidity (TA), fat, and protein. Many genera were significantly correlated with TA, for example Acinetobacter (R = 0.426), Enhydrobacter (R = 0.309), Chryseobacterium (R = 0.352), Lactobacillus (R = −0.326), norank_o__DTU014 (R = −0.697), norank_f__SC-I-84 (R = −0.678), and Subgroup_10 (R = −0.721). Additionally, norank_f__ Muribaculaceae was moderately negatively correlated with fat (R = −0.476) and protein (R = −0.513). These findings provide new information on the ecology of raw milk microbiota at the farm level and contribute to the understanding of the variation in raw milk microbiota in China. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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21 pages, 7569 KiB  
Article
Effect of Adding Bifidobacterium animalis BZ25 on the Flavor, Functional Components and Biogenic Amines of Natto by Bacillus subtilis GUTU09
by Qifeng Zhang, Guangqun Lan, Xueyi Tian, Laping He, Cuiqin Li, Han Tao, Xuefeng Zeng and Xiao Wang
Foods 2022, 11(17), 2674; https://doi.org/10.3390/foods11172674 - 02 Sep 2022
Cited by 4 | Viewed by 2152
Abstract
Natto is a high-value fermented soybean produced by B. subtilis. However, B. subtilis produces a pungent amine odor. This study compared the volatile organic compounds (VOCs), free amino acids (FAAs) and biogenic amines (BAs), nattokinase (NK) of natto made by two-strain fermentation [...] Read more.
Natto is a high-value fermented soybean produced by B. subtilis. However, B. subtilis produces a pungent amine odor. This study compared the volatile organic compounds (VOCs), free amino acids (FAAs) and biogenic amines (BAs), nattokinase (NK) of natto made by two-strain fermentation with Bifidobacterium animalis BZ25 and Bacillus subtilis GUTU09 (NMBB) and that of natto made by single-strain fermentation with Bacillus subtilis GUTU09 (NMB). Compared with NMB, volatile amine substances disappeared, ketones and aldehydes of NMBB were reduced, and alcohols increased. Besides that, the taste activity value of other bitter amino acids was lowered, and BA content was decreased from 255.88 mg/kg to 238.35 mg/kg but increased NK activity from 143.89 FU/g to 151.05 FU/g. Correlation analysis showed that the addition of BZ25 reduced the correlation between GUTU09 and BAs from 0.878 to 0.808, and pH was changed from a positive correlation to a negative one. All these results showed that the quality of natto was improved by two-strain co-fermentation, which laid a foundation for its potential industrial application. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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Review

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17 pages, 2060 KiB  
Review
What Are the Main Factors That Affect the Flavor of Sauce-Aroma Baijiu
by Jiao Niu, Shiqi Yang, Yi Shen, Wei Cheng, Hehe Li, Jinyuan Sun, Mingquan Huang and Baoguo Sun
Foods 2022, 11(21), 3534; https://doi.org/10.3390/foods11213534 - 07 Nov 2022
Cited by 14 | Viewed by 3070
Abstract
Sauce-aroma Baijiu is a distilled Baijiu well-known in China, and features a unique sauce-aroma style formed by a complex producing process in a specific geographical environment. However, there are few comprehensive reviews of the factors influencing the formation of its flavor. To this [...] Read more.
Sauce-aroma Baijiu is a distilled Baijiu well-known in China, and features a unique sauce-aroma style formed by a complex producing process in a specific geographical environment. However, there are few comprehensive reviews of the factors influencing the formation of its flavor. To this end, reviews are hereby carried out over factors including different components in brewing raw materials, geographical environment of Baijiu production, brewing technology including the production of high-temperature Daqu and the brewing process, storage technology including the type of storage containers, storage time and storage temperature involved in the production of Sauce-aroma Baijiu. In addition, the effects of these factors on the flavor formation of Sauce-aroma Baijiu are also revealed, providing references and forging a foundation for stabilizing and improving the quality of Sauce-aroma Baijiu. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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23 pages, 2065 KiB  
Review
Characterization, High-Density Fermentation, and the Production of a Directed Vat Set Starter of Lactobacilli Used in the Food Industry: A Review
by Yun Lu, Shuqi Xing, Laping He, Cuiqin Li, Xiao Wang, Xuefeng Zeng and Yifeng Dai
Foods 2022, 11(19), 3063; https://doi.org/10.3390/foods11193063 - 02 Oct 2022
Cited by 10 | Viewed by 3752
Abstract
Lactobacilli have been widely concerned for decades. Bacteria of the genus Lactobacillus have been commonly employed in fermented food to improve the appearance, smell, and taste of food or prolong its shelf-life. They comprise 261 species (by March 2020) that are highly diverse [...] Read more.
Lactobacilli have been widely concerned for decades. Bacteria of the genus Lactobacillus have been commonly employed in fermented food to improve the appearance, smell, and taste of food or prolong its shelf-life. They comprise 261 species (by March 2020) that are highly diverse at the phenotypic, ecological, and genotypic levels. Some Lactobacilli strains have been documented to be essential probiotics, which are defined as a group of living microorganisms that are beneficial to the health of the host when ingested in sufficiency. However, the characterization, high-density fermentation, and the production of a directed vat set (DVS) starter of Lactobacilli strains used in the food industry have not been systematically reported. This paper mainly focuses on reviewing Lactobacilli as functional starter cultures in the food industry, including different molecular techniques for identification at the species and strain levels, methods for evaluating Lactobacilli properties, enhancing their performance and improving the cell density of Lactobacilli, and the production techniques of DVS starter of Lactobacilli strains. Moreover, this review further discussed the existing problems and future development prospects of Lactobacilli in the food industry. The viability and stability of Lactobacilli in the food industry and gastrointestinal environment are critical challenges at the industrial scale. The new production equipment and technology of DVS starter of Lactobacilli strains will have the potential for large-scale application, for example, developing low-temperature spray drying, freezing granulation drying, and spray freeze-drying. Full article
(This article belongs to the Special Issue Molecular Methods in Food Quality and Microbiological Safety)
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