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Food Quality Control: Microbial Diversity and Metabolic Regulation

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

Deadline for manuscript submissions: closed (10 October 2024) | Viewed by 21786

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Dr. Wanping Chen

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Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany
Interests: fungi; Asepergillus; secondary metabolites; food fermentation
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Dr. Bin Wang

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School of Food Science and Technology, Shihezi University, Shihezi, China
Interests: microbiology; transcriptome; genome; metabolome; proteome
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Prof. Dr. Xuewei Shi

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School of Food Science and Technology, Shihezi University, Shihezi, China
Interests: microbiology; food fermentation; secondary metabolites; metagenomics; flavors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Food quality control is always a hot topic in the food industry, especially in fermented foods. During food fermentation, microbial communities vary with regular processes, accompanied by converting substrates, such as carbohydrates, proteins, and lipids, into raw materials and beneficial metabolites (organic acids, alcohols, amino acids, peptides, fatty acids, etc.). These beneficial metabolites have a main nutritional composition and sensory and functional properties. Obviously, microbial diversity and metabolic regulation in fermented foods have become the main factors controlling food quality.

Therefore, this Special Issue aims to present recent advances in microbial diversity and the metabolic regulation of fermented foods. We encourage the submission of manuscripts that include, but are not limited to:

the succession of microbial communities during food fermentation;
dynamic changes in organoleptic, nutritional, and functional characteristics during food processing;
the relationship between microbes and the metabolic activities of fermented products;
the effects of microbes on food safety and quality;
main metabolisms and their regulation during food fermentation;
the industrial transformation of traditional fermented food;
screening and applying functional microbes;
the correlation of microbes with environment and gut health;
the development of characteristic functional metabolites in fermented foods.

Dr. Wanping Chen
Dr. Bin Wang
Prof. Dr. Xuewei Shi
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

food fermentation
microbial diversity
food quality
metabolic engineering
metabolic regulation
food microbiology
microbe application
food flavors

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Published Papers (10 papers)

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Research

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16 pages, 8672 KiB

Open AccessArticle

Characterizing the Contribution of Strain Specificity to the Microbiota Structure and Metabolites of Muqu and Fresh High-Temperature Daqu

by Yi Zhang, Zhu Zhang, Jun Huang, Rongqing Zhou, Qiuxiang Tang and Yao Jin

Foods 2024, 13(19), 3098; https://doi.org/10.3390/foods13193098 - 27 Sep 2024

Cited by 2 | Viewed by 1059

Abstract

In this study, the differences in physicochemical properties, microbial community structure, and metabolic characteristics between various fortified Muqu and their corresponding high-temperature Daqu (HTD) were investigated using multiphase detection methods. The results demonstrated that the physicochemical properties, community structure, dominant bacterial composition, and metabolic components varied significantly among the different types of fortified HTD. The differences between HTDs became more pronounced when fortified HTD was used as Muqu. Compared to HTD, Muqu exhibited a more complex volatile profile, while HTD contained higher levels of characteristic non-volatile components. The cultivable bacteria count in Muqu was significantly higher than that in HTD, while the cultivable fungi count was slightly lower than that in HTD. The fungal profiles in HTD were primarily associated with starch hydrolysis and ethanol synthesis, while bacterial activity was more prominent in Muqu. Additionally, pyrazine synthesis was mainly attributed to fungi in Muqu and bacteria in HTD. Source Tracker analysis indicated that 8.11% of the bacteria and 26.76% of the fungi originated from Muqu. This study provides a theoretical foundation for the controlled production of HTD, contributing to improvements in its quality and consistency. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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14 pages, 7711 KiB

Open AccessArticle

Insights into the Correlation between Microbial Community Succession and Pericarp Degradation during Pepper (Piper nigrum L.) Peeling Process via Retting

by Yuting Fu, Shuai Chen, Xinjun Wang, Lu Wang, Zexin Wang, Yanfei Cheng, Yuyi Liu, Lin Zhang, Sixin Liu, Jiamu Kang and Congfa Li

Foods 2024, 13(11), 1615; https://doi.org/10.3390/foods13111615 - 23 May 2024

Cited by 1 | Viewed by 1324

Abstract

White pepper, used both as a seasoning in people’s daily diets and as a medicinal herb, is typically produced by removing the pericarp of green pepper through the retting process. However, the mechanism of the retting process for peeling remains unclear. Therefore, this study aimed to investigate the changes in physicochemical factors, microbial community succession effects, and metabolites of the pepper pericarp during the pepper peeling process. The findings indicated that pre-treatment involving physical friction before the retting process effectively reduced the production time of white pepper. During the retting process, the pectinase activity increased, leading to a decrease in the pectin content in the pepper pericarp. There was a significant correlation observed between the changes in pH, pectin content, and peeling rate and the Shannon diversity index of bacteria and fungi. Prevotella, Lactococcus, and Candida were the dominant microbial genera during the retting. The functional predictions suggested that the monosaccharides degraded from the pepper pericarp could have been utilized by microbes through sugar metabolism pathways. Metabolomic analysis showed that the metabolic pathways of carbohydrates and amino acids were the main pathways altered during the pepper peeling process. The verification experiment demonstrated that the degradation of pectin into galacturonic acid by polygalacturonase was identified as the key enzyme in shortening the pepper peeling time. The structure of the pepper pericarp collapsed after losing the support of pectin, as revealed by scanning electron microscopy. These results suggest that the decomposition of the pepper pericarp was driven by key microbiota. The succession of microbial communities was influenced by the metabolites of the pepper pericarp during retting. These findings provide new insights into the retting process and serve as an important reference for the industrial production of white pepper. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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16 pages, 2660 KiB

Open AccessArticle

Co-regulation of Thermosensor Pathogenic Factors by C-di-GMP-Related Two-Component Systems and a cAMP Receptor-like Protein (Clp) in Stenotrophomonas maltophilia

by Jieqiong Ding, Minghong Liao and Qingling Wang

Foods 2024, 13(8), 1201; https://doi.org/10.3390/foods13081201 - 15 Apr 2024

Viewed by 1614

Abstract

Stenotrophomonas maltophilia is a major threat to the food industry and human health owing to its strong protease production and biofilm formation abilities. However, information regarding regulatory factors or potential mechanisms is limited. Herein, we observed that temperature differentially regulates biofilm formation and protease production, and a cAMP receptor-like protein (Clp) negatively regulates thermosensor biofilm formation, in contrast to protease synthesis. Among four c-di-GMP-related two-component systems (TCSs), promoter fusion analysis revealed that clp transcription levels were predominantly controlled by LotS/LotR, partially controlled by both RpfC/RpfG and a novel TCS Sm0738/Sm0737, with no obvious effect caused by Sm1912/Sm1911. Biofilm formation in Δclp and ΔTCSs strains suggested that LotS/LotR controlled biofilm formation in a Clp-mediated manner, whereas both RpfC/RpfG and Sm0738/Sm0737 may occur in a distinct pathway. Furthermore, enzymatic activity analysis combined with c-di-GMP level indicated that the enzymatic activity of c-di-GMP-related metabolism proteins may not be a vital contributor to changes in c-di-GMP level, thus influencing physiological functions. Our findings elucidate that the regulatory pathway of c-di-GMP-related TCSs and Clp in controlling spoilage or the formation of potentially pathogenic factors in Stenotrophomonas expand the understanding of c-di-GMP metabolism and provide clues to control risk factors of S. maltophilia in food safety. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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18 pages, 3917 KiB

Open AccessArticle

The Biotransformation and Influence on the Functional Activities of Metabolites during the Fermentation of Elaeagnus moorcroftii Wall.ex Schlecht. Juice by Bifidobacterium animalis subsp. lactis HN-3

by Yixuan Wang, Chenxi Wang, Zhenghui Lan, Yingdi Teng, Yongqing Ni and Yan Zhang

Foods 2024, 13(6), 926; https://doi.org/10.3390/foods13060926 - 19 Mar 2024

Cited by 3 | Viewed by 1731

Abstract

Elaeagnus moorcroftii Wall.ex Schlecht. (EWS) has extensive nutrients and functional active ingredients, which makes it an excellent potential substrate for fermentation. The improvement in the antioxidant activity of Elaeagnus moorcroftii Wall.ex Schlecht. juice (EWSJ) fermented by Bifidobacterium animalis subsp. lactis HN-3 (B.an3) could be attributed to the metabolism and biotransformation of plant-based products by the bacterial strain. To reveal the underlying mechanism, non-targeted metabolomics was applied in this study. After fermentation, the structure of downregulated carbohydrates, amino acids, fatty acids, and flavonoids was changed by Bifidobacterium biotransformation (included four reductions, three hydrolyses, four isomerizations, three deglycosidations, and five other reactions). The structure of these converted upregulated products has a higher antioxidant ability to reduce free radicals than their precursors, such as the flavonoids in the form of hydrolyzed conjugates, amino acids with multiple sulfhydryls or hydroxys, carbohydrates with reactive oxygen on benzene rings and fatty acids with unsaturated bonds, short chains, and glycosides. These findings shed light on the mechanism of the metabolism and biotransformation of EWSJ by B.an3, facilitate the study of the interaction between probiotics and fermented plant-based products, and provide a theoretical basis for the development of Bifidobacterium-fermented plant products with stronger functional activities. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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20 pages, 22928 KiB

Open AccessArticle

Investigation of Acid Tolerance Mechanism of Acetobacter pasteurianus under Different Concentrations of Substrate Acetic Acid Based on 4D Label-Free Proteomic Analysis

by Tian Li, Xinwei Wang, Chunyan Li, Qingquan Fu, Xuewei Shi and Bin Wang

Foods 2023, 12(24), 4471; https://doi.org/10.3390/foods12244471 - 13 Dec 2023

Cited by 1 | Viewed by 1680

Abstract

Acetobacter pasteurianus is always used to brew vinegar because of its ability of producing and tolerating a high concentration of acetic acid. During vinegar fermentation, initial acetic acid contributes to acetic acid accumulation, which varies with initial concentrations. In this study, to investigate the mechanisms of tolerating and producing acetic acid of Acetobacter pasteurianus under different concentrations of substrate acetic acid, four-dimensional label-free proteomic technology has been used to analyze the protein profiles of Acetobacter pasteurianus at different growth stages (the lag and exponential phases) and different substrate acetic acid concentrations (0%, 3%, and 6%). A total of 2093 proteins were quantified in this study. The differentially expressed proteins were majorly involved in gene ontology terms of metabolic processes, cellular metabolic processes, and substance binding. Under acetic acid stress, strains might attenuate the toxicity of acetic acid by intensifying fatty acid metabolism, weakening the tricarboxylic acid cycle, glycerophospholipid and energy metabolism during the lag phase, while strains might promote the assimilation of acetic acid and inter-conversion of substances during the exponential phase by enhancing the tricarboxylic acid cycle, glycolysis, pyruvate, and energy metabolism to produce and tolerate acid. Besides, cell cycle regulation and protein translation might be potential acid tolerance pathways under high acid stress. The result contributes to the exploration of new potential acid tolerance mechanisms in Acetobacter pasteurianus from four-dimensional label-free relative quantitative proteomics analysis. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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20 pages, 5471 KiB

Open AccessArticle

Metagenomic Insights into the Regulatory Effects of Microbial Community on the Formation of Biogenic Amines and Volatile Flavor Components during the Brewing of Hongqu Rice Wine

by Ziyi Yang, Wenlong Li, Yujie Yuan, Zihua Liang, Yingyin Yan, Ying Chen, Li Ni and Xucong Lv

Foods 2023, 12(16), 3075; https://doi.org/10.3390/foods12163075 - 16 Aug 2023

Cited by 11 | Viewed by 2507

Abstract

As one of the typical representatives of Chinese rice wine (Huangjiu), Hongqu rice wine is produced with glutinous rice as the main raw material and Hongqu as the fermentation starter. The complex microbial flora in the brewing process may have a great influence on the formation of the flavor quality and drinking safety of Hongqu rice wine. Previous studies have shown that high biogenic amine (BA) content in rice wine has potential physiological toxicity and has become a bottleneck problem restricting the development of the rice wine industry. This study aimed to evaluate the regulatory effects of the microbial community on the formation of BAs and volatile flavor components during the brewing of Hongqu rice wine. The results demonstrated that histamine, putrescine, cadaverine, tyramine, tryptamine, spermine, and spermidine were the main BAs in Hongqu rice wine. The contents of putrescine, cadaverine, histamine, tyramine, and spermidine in Hongqu rice wine of HBAs (with higher BAs content) were significantly higher than those in LBAs (with lower BAs content). GC-MS testing results showed that there were significant differences in the composition of volatile organic compounds (VOCs) between HBAs and LBAs. Among them, VOCs such as 2-methoxy-4-vinylphenol, ethyl caprate, phenethyl acetate, ethyl lactate, ethyl myristate, ethyl palmitate, ethyl n-octadecanoate, ethyl oleate, and ethyl linoleate were identified as the characteristic volatile components with significant differences between HBAs and LBAs. Microbiome analysis based on metagenomic sequencing revealed that unclassified_g_Pantoea, Klebsiella pneumoniae, Panobacter disperse, unclassified_f_Enterobacteriaceae, Leuconostoc mesenteroides, and Saccharomyces cerevisiae were the dominant microbial species in the HBA brewing process, while Weissella confuse, Pediococcus acidilactici, Saccharomyces cerevisiae, and Aspergillus niger were the dominant microbial species in the LBA brewing process. Furthermore, correlation heatmap analysis demonstrated that BAs were positively related to Lactobacillus curvatus, Lactococcus lactis, and Leuconostoc mesenteroides. Bioinformatical analysis based on the KEGG database revealed that the microbial genes encoding enzymes involved in BAs’ synthesis were more abundant in HBAs, and the abundances of microbial genes encoding enzymes related to BAs’ degradation and the metabolism of characteristic volatile components were higher in LBAs. Overall, this work provides important scientific data for enhancing the flavor quality of Hongqu rice wine and lays a solid foundation for the healthy development of the Hongqu rice wine industry. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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14 pages, 4205 KiB

Open AccessArticle

Microbial Community Dynamics and the Correlation between Specific Bacterial Strains and Higher Alcohols Production in Tartary Buckwheat Huangjiu Fermentation

by Sheng Yin, Mingquan Huang, Jiaxuan Wang, Bo Liu and Qing Ren

Foods 2023, 12(14), 2664; https://doi.org/10.3390/foods12142664 - 11 Jul 2023

Cited by 5 | Viewed by 1754

Abstract

Tartary buckwheat is a healthy grain rich in nutrients and medicinal ingredients and consequently is commonly used for Huangjiu brewing. In order to reveal the correlation between microbial succession and higher alcohols production, in this study, Huangjiu fermentation was conducted using Tartary buckwheat as the raw material and wheat Qu as the starter culture. Microbial community dynamics analysis indicated that the bacterial diversity initially decreased rapidly to a lower level and then increased and maintained at a higher level during fermentation. Lactococcus was the dominant bacteria and Ralstonia, Acinetobacter, Cyanobacteria, and Oxalobacteraceae were the bacterial genera with higher abundances. In sharp contrast, only 13 fungal genera were detected during fermentation, and Saccharomyces showed the dominant abundance. Moreover, 18 higher alcohol compounds were detected by GC-MS during fermentation. Four compounds (2-phenylethanol, isopentanol, 1-hexadecanol, and 2-phenoxyethanol) were stably detected with high concentrations during fermentation. The compound 2-ethyl-2-methyl-tridecanol was detected to be of the highest concentration in the later period of fermentation. Correlation analysis revealed that the generation of 2-phenylethanol, isopentanol, 1-hexadecanol, and 2-phenoxyethanol were positively correlated with Granulicatella and Pelomonas, Bacteroides, Pseudonocardia and Pedomicrobium, and Corynebacterium, respectively. The verification fermentation experiments indicated that the improved wheat Qu QT3 and QT4 inoculated with Granulicatella T3 and Acidothermus T4 led to significant increases in the contents of 2-phenylethanol and pentanol, as well as isobutanol and isopentanol, respectively, in the Tartary buckwheat Huangjiu. The findings benefit understanding of higher alcohols production and flavor formation mechanisms in Huangjiu fermentation. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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19 pages, 8930 KiB

Open AccessArticle

Flavor Characterization of Native Xinjiang Flat Peaches Based on Constructing Aroma Fingerprinting and Stoichiometry Analysis

by Chunyan Li, Youyou Xu, Huimin Wu, Ruirui Zhao, Xinwei Wang, Fangfang Wang, Qingquan Fu, Tiantian Tang, Xuewei Shi and Bin Wang

Foods 2023, 12(13), 2554; https://doi.org/10.3390/foods12132554 - 29 Jun 2023

Cited by 10 | Viewed by 2019

Abstract

The flat peach is a high economic value table fruit possessing excellent quality and a unique aroma. This article investigated the quality characteristics and aroma fingerprinting of flat peaches (Qingpan, QP; Ruipan 2, R2; Ruipan 4, R4; Wanpan, WP) from Xinjiang in terms of taste, antioxidant capacity, and volatile aroma compounds using high-performance liquid chromatography (HPLC) and HS-SPME-GC-MS. The results showed that the flat peaches had a good taste and high antioxidant capacity, mainly due to the high sugar–low acid property and high levels of phenolic compounds. This study found that sucrose (63.86~73.86%) was the main sugar, and malic acid (5.93~14.96%) and quinic acid (5.25~15.01%) were the main organic acids. Furthermore, chlorogenic acid (main phenolic compound), epicatechin, rutin, catechin, proanthocyanidin B1, and neochlorogenic acid were positively related to the antioxidant activity of flat peaches. All flat peaches had similar aroma characteristics and were rich in aromatic content. Aldehydes (especially benzaldehyde and 2-hexenal) and esters were the main volatile compounds. The aroma fingerprinting of flat peaches consisted of hexanal, 2-hexenal, nonanal, decanal, benzaldehyde, 2,4-decadienal, dihydro-β-ionone, 6-pentylpyran-2-one, 2-hexenyl acetate, ethyl caprylate, γ-decalactone, and theaspirane, with a “peach-like”, “fruit”, and “coconut-like” aroma. Among them, 2,4-decadienal, 2-hexenyl acetate, and theaspirane were the characteristic aroma compounds of flat peaches. The results provide a theoretical basis for the industrial application of the special aroma of flat peaches. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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13 pages, 3324 KiB

Open AccessArticle

The Effect of Buckwheat Resistant Starch on Intestinal Physiological Function

by Zhan-Bin Sun, Xiao Zhang, Yi Yan, Jia-Liang Xu, Xin Lu and Qing Ren

Foods 2023, 12(10), 2069; https://doi.org/10.3390/foods12102069 - 21 May 2023

Cited by 7 | Viewed by 4793

Abstract

Resistant starch appears to have promising effects on hypertension, cardiovascular and enteric illness. The influence of resistant starch on intestinal physiological function has drawn great attention. In this study, we first analyzed the physicochemical characteristics, including the crystalline properties, amylose content, and anti-digestibility among different types of buckwheat-resistant starch. The influence of resistant starch on the physiological functions of the mouse intestinal system, contained defecation, and intestinal microbes were also evaluated. The results showed that the crystalline mold of buckwheat-resistant starch changed from A to B + V after acid hydrolysis treatment (AHT) and autoclaving enzymatic debranching treatment (AEDT). The amylose content in AEDT was higher than in AHT and raw buckwheat. Moreover, the anti-digestibility of AEDT was also stronger than that in AHT and raw buckwheat. The buckwheat-resistant starch can promote bowel intestinal tract movement. The quantity of intestinal microbe was regulated by buckwheat-resistant starch. Our research demonstrates an effective preparation method for improving the quality of buckwheat-resistant starch and found that buckwheat-resistant starch has the role of adjusting the distribution of the intestinal flora and maintaining the health of the body. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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Review

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17 pages, 1474 KiB

Open AccessReview

The Complexity of Chinese Cereal Vinegar Flavor: A Compositional and Sensory Perspective

by Hong Zhu, Kehong Liang, Dazhou Zhu, Junmao Sun and Ju Qiu

Foods 2024, 13(5), 756; https://doi.org/10.3390/foods13050756 - 29 Feb 2024

Cited by 4 | Viewed by 2007

Abstract

With a millennium-long history, traditional Chinese cereal vinegar (CCV) is a significant part of China’s cultural heritage. The unique flavor of CCV is derived from the use of cereal and its bran as raw materials and solid-state fermentation as a brewing technique. This paper systemically summarized recent research progress on the aroma compounds in CCV, the biochemical generation of aroma compounds during the brewing process, and the association between sensory perception and the primary aroma compounds. Furthermore, a complete CCV lexicon and sensory wheel prototype were constructed. This study aims to lay a foundation for future CCV aroma research, quality improvement, and industrialization. Full article

(This article belongs to the Special Issue Food Quality Control: Microbial Diversity and Metabolic Regulation)

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