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Fermentation
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Perspectives on Microbial Ecology of Fermented Foods
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Perspectives on Microbial Ecology of Fermented Foods

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation for Food and Beverages".

Deadline for manuscript submissions: closed (20 September 2023) | Viewed by 13229

Special Issue Editors

Dr. Kai Zhong

E-Mail Website
Guest Editor
College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
Interests: fermented foods; food microbiology; lactic acid bacteria; Bacillus spp.; microbial communities; food quality; flavor compounds; food safety
Special Issues, Collections and Topics in MDPI journals
Dr. Zhihua Li

E-Mail Website
Guest Editor
Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
Interests: flavor chemistry; food chemistry; food analysis; food microbiology; traditional fermented foods
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fermented foods are largely consumed by people all over the world because of their unique flavors and health benefits. Their qualities, flavors, and health benefits are mainly dependent on the metabolic activity of microbial communities during the fermentation process. Generally, the microbial ecology in fermented foods changed as fermentation proceeded, thus resulting in distinct microbial metabolites at different stages of fermentation, and these different metabolites will endow a unique flavor and quality to the final fermented products. Even in the same kind of fermented food, this distinct microbial ecology also exists because of the differences in the origin of raw materials and production environment. Moreover, microbial ecology has positively correlated with the quality, safety, and flavor of fermented foods. Recently, it has been reported that raw materials and inoculation of core microorganisms can enhance the quality, safety, and flavor, as well as change the microbial ecology during the fermentation process of fermented foods. Thus, research on the diverse functions of microbial ecology on fermented foods and the related mechanism needs to be further elucidated. In this Special Issue, we kindly invite you to submit comprehensive reviews, research articles, and short communications on the effects of the microbial ecology of fermented foods, including the formation mechanism of fermented foods’ unique flavor and quality, the relationship between core microorganisms and the quality of fermented foods, and the dynamic change in microbial ecology during fermentation, as well as the microbial interactions in the fermentation system.

Dr. Kai Zhong
Dr. Zhihua Li
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. Fermentation is an international peer-reviewed open access monthly 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 2600 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

  • fermented foods
  • microbial ecology
  • microbial community
  • microbial interaction
  • food quality
  • food safety
  • food flavor
  • probiotic microorganisms
  • lactic acid bacteria
  • yeast

Published Papers (6 papers)

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Research

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16 pages, 1483 KiB  
Article
Investigating Yeast–Lactobacilli Interactions through Co-Culture Growth and Metabolite Analysis
by Stefano Nenciarini, Ana Reis-Costa, Marco Pallecchi, Sonia Renzi, Aldo D’Alessandro, Agnese Gori, Benedetta Cerasuolo, Niccolò Meriggi, Gian Luca Bartolucci and Duccio Cavalieri
Fermentation 2023, 9(11), 933; https://doi.org/10.3390/fermentation9110933 - 26 Oct 2023
Cited by 1 | Viewed by 1456
Abstract
The various forms of interactions that microorganisms engage in within fermented foods result in distinct metabolic product patterns. Fermentation products often feature both yeasts and bacteria, each possessing characteristics that can enhance the overall quality of the food, thus benefiting consumers. Kefir, a [...] Read more.
The various forms of interactions that microorganisms engage in within fermented foods result in distinct metabolic product patterns. Fermentation products often feature both yeasts and bacteria, each possessing characteristics that can enhance the overall quality of the food, thus benefiting consumers. Kefir, a fermented milk originating from grains containing a unique and intricate blend of bacteria and yeasts living in a symbiotic relationship, is a valuable model for studying the evolution of the interactions between yeasts and bacteria. Targeted metagenomics was applied to investigate the microbiome of a batch of traditional Romanian kefir and further examine the growth and metabolic properties of the dominant yeast and bacterial strains isolated from this batch. In contrast to yeast, which is either unaffected or harmed by the presence of bacteria, our study revealed that a specific strain of Lactobacillus (L. rhamnosus) derived from the kefir batch benefited from the presence of Saccharomyces cerevisiae. The analysis of short-chain fatty acids (SCFAs) produced by in vitro cultures of these two chosen strains indicated significant changes in SCFA levels compared to single cultures. The dynamic interactions described in this and other studies on kefir emphasize the importance of a more profound comprehension of the ecological mechanisms governing interactions between yeast, bacterial, and mammalian cells. Full article
(This article belongs to the Special Issue Perspectives on Microbial Ecology of Fermented Foods)
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12 pages, 2386 KiB  
Article
Microbial Community Profiling from Natural Whey Starter to Mozzarella among Different Artisanal Dairy Factories in Apulia Region (Italy)
by Stefano Castellana, Angelica Bianco, Loredana Capozzi, Laura Del Sambro, Domenico Simone, Marco Iammarino, Valeria Nardelli, Annamaria Caffò, Carmelinda Trisolini, Antonella Castellana, Elisabetta Catalano, Angelica Milano, Giulia Schino, Roldano Sottili and Antonio Parisi
Fermentation 2023, 9(10), 911; https://doi.org/10.3390/fermentation9100911 - 16 Oct 2023
Viewed by 1338
Abstract
Mozzarella is one of the most popular unripened Apulian cheeses. Knowledge about microbial composition and variability of artisanal mozzarella and its production chain is increasingly growing. In this study, microbial communities from natural whey starters to end products from four renowned Apulian artisanal [...] Read more.
Mozzarella is one of the most popular unripened Apulian cheeses. Knowledge about microbial composition and variability of artisanal mozzarella and its production chain is increasingly growing. In this study, microbial communities from natural whey starters to end products from four renowned Apulian artisanal dairy factories have been explored by means of 16S metagenomics. The chemical properties of mozzarella samples were also detected and analyzed. Lactobacillus is the core acidifying component of the used starters, while some psychrophilic or contaminants bacteria appear in site-specific products. Biodiversity was found to be quite similar between the whey and mozzarella sample pools, while a significant variability among production sites (factories) has been detected. Furthermore, mozzarella microbial diversity seems to be in positive correlation with its lactic acid content. Targeted metagenomics would then be a powerful and relatively quick technique to characterize the microbiological variability of traditional milk-based foods. Full article
(This article belongs to the Special Issue Perspectives on Microbial Ecology of Fermented Foods)
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11 pages, 3091 KiB  
Article
Exploration of Microbial Community Diversity and Bioactive Substances during Fermentation of Mulberry Jiaosu, an Edible Naturally Fermented Mulberry Product
by Jing Zhang, Minhui Zhao, Yuan Yi, Yifen Huang, Qianqian Yin and Yong Zuo
Fermentation 2023, 9(10), 910; https://doi.org/10.3390/fermentation9100910 - 16 Oct 2023
Cited by 1 | Viewed by 1038
Abstract
Mulberry Jiaosu, derived from natural fermentation using fresh mulberry fruit as a raw material, refers to an edible product containing specific bioactive substances. However, the dynamic changes in the bioactive substances of organic acids, amino acids and polyphenols as well as the species [...] Read more.
Mulberry Jiaosu, derived from natural fermentation using fresh mulberry fruit as a raw material, refers to an edible product containing specific bioactive substances. However, the dynamic changes in the bioactive substances of organic acids, amino acids and polyphenols as well as the species and function of microorganisms in mulberry Jiaosu are still not clear. Herein, the whole fermentation process of mulberry Jiaosu was comprehensively researched by analyzing the microbial community structure and bioactive substances. The results showed that the change in physicochemical parameters mainly happened within 30 days of fermentation. The total organic acids and total polyphenols presented upward trends. Total amino acids were partly consumed during the fermentation. A total of 173 fungal genera and 295 bacterial genera were detected in mulberry Jiaosu, mainly including Torulaspora, Zygosaccharomyces and Lactobacillus, whose abundance can be influenced by changes in the fermentation environment. During the fermentation of mulberry Jiaosu, 8 organic acids, 17 amino acids and 9 polyphenols were observed, which could be regulated by the metabolism of microorganisms. Zygosaccharomyces exhibited positive correlations with the majority of the organic acids, amino acids and polyphenols, presenting a great influence on the formation of bioactive substances. Compared with fungi, bacteria contributed more to the synthesis of organic acids, free amino acids and polyphenols. This study revealed the bioactive substances and microbial diversity during the fermentation of mulberry Jiaosu, which are findings that will contribute to the precise regulation of the fermentation process and improvement of the product quality. Full article
(This article belongs to the Special Issue Perspectives on Microbial Ecology of Fermented Foods)
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15 pages, 2799 KiB  
Article
Effects of Low-Temperature and Low-Salt Fermentation on the Physicochemical Properties and Volatile Flavor Substances of Chinese Kohlrabi Using Gas Chromatography–Ion Mobility Spectrometry
by Hongfan Chen, Xin Nie, Tao Peng, Lu Xiang, Dayu Liu, Huailiang Luo and Zhiping Zhao
Fermentation 2023, 9(2), 146; https://doi.org/10.3390/fermentation9020146 - 01 Feb 2023
Cited by 7 | Viewed by 1803
Abstract
To explore the effect of low-temperature and low-salt fermentation on the volatile flavor substances of Chinese kohlrabi, low-temperature and low-salt fermented Chinese kohlrabi (LSCK) and traditional high-salt fermented Chinese kohlrabi (HSCK) were produced. The physicochemical and texture properties of the two kinds of [...] Read more.
To explore the effect of low-temperature and low-salt fermentation on the volatile flavor substances of Chinese kohlrabi, low-temperature and low-salt fermented Chinese kohlrabi (LSCK) and traditional high-salt fermented Chinese kohlrabi (HSCK) were produced. The physicochemical and texture properties of the two kinds of Chinese kohlrabies were evaluated. Headspace gas chromatography-ion mobility spectrometry (GC-IMS) and electronic nose (E-nose) were used to analyze the volatile flavor substances of the kohlrabi. The results showed that the total acid content significantly decreased (p < 0.05), while protein and reducing sugar contents significantly increased (p < 0.05) by low-temperature and low-salt fermentation. A total of 114 volatile flavor substances were identified. The alcohol, ketone, pyrazine, ether, and nitrile contents in LSCK were significantly higher than those in HSCK (p < 0.05). Moreover, the unpleasant flavor from the 3-methylbutyric acid formation was effectively depressed in LSCK. The principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA) models established by multivariate statistical analysis significantly distinguished the two types of kohlrabies. Multivariate statistical analysis suggested that 16 volatile flavor substances with VIP >1, including tetrahydrothiophene, ethyl 3-(methylthio)propanoate, 3-methylbutyric acid, hexanenitrile, and 3-methyl-3-buten-1-ol, could be used as potential biomarkers for identifying LSCK and HSCK. The E-nose analysis further demonstrated that there was a significant difference in overall flavor between the LSCK and HSCK. The present study provides support for the development of green processing technology and new low-salt Chinese kohlrabi products. Full article
(This article belongs to the Special Issue Perspectives on Microbial Ecology of Fermented Foods)
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Review

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13 pages, 965 KiB  
Review
Microbial Composition, Bioactive Compounds, Potential Benefits and Risks Associated with Kombucha: A Concise Review
by Abidemi Oluranti Ojo and Olga de Smidt
Fermentation 2023, 9(5), 472; https://doi.org/10.3390/fermentation9050472 - 13 May 2023
Cited by 3 | Viewed by 3636
Abstract
Kombucha is a fermented tea beverage containing bioactive compounds from tea and vital compounds such as acetic acid, D-saccharic acid-1,4-lactone, and glucuronic and gluconic acids produced from the metabolic activities of bacteria and yeasts, which benefit human health. Kombucha contains a symbiotic culture [...] Read more.
Kombucha is a fermented tea beverage containing bioactive compounds from tea and vital compounds such as acetic acid, D-saccharic acid-1,4-lactone, and glucuronic and gluconic acids produced from the metabolic activities of bacteria and yeasts, which benefit human health. Kombucha contains a symbiotic culture of bacteria and yeast (SCOBY), which actively ferments sugar. Kombucha microbial compositions vary due to environmental conditions and the starter culture. Saccharomyces sp., Schizosaccharomyces pombe, Schizosaccharomyces sp., and Brettanomyces sp. (yeasts) and Acetobacter aceti, Komagataeibacter xylinum (formerly known as Gluconacetobacter xylinum), Gluconobacter oxydans, and Acetobacter pasteurianus (acetic acid-producing bacteria) are commonly found in kombucha. This review focused on the microbial compositions of kombucha and their functionality. Aspects discussed include: (i). developments in kombucha, (ii). microbial compositions of kombucha, (ii). microbial production of kombucha cellulose, (iv). factors influencing kombucha microbial compositions, (v). tea type and kombucha bioactive compounds, (vi). kombucha health benefits, and (v). potential risk factors of kombucha consumption. Current gaps, recommendations, and prospects were also discussed. Kombucha production using rooibos as the tea base is recommended, as rooibos is caffeine-free. Upcycling kombucha wastes, mainly SCOBY, for producing cellulose filters, improving food flavors and as a substrate in food fermentations is touched on. Full article
(This article belongs to the Special Issue Perspectives on Microbial Ecology of Fermented Foods)
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17 pages, 1106 KiB  
Review
Phages in Fermented Foods: Interactions and Applications
by Qian Wu, Luming Li, Peng Xiang, Ting Zhang, Lianxin Peng, Liang Zou and Qiang Li
Fermentation 2023, 9(3), 201; https://doi.org/10.3390/fermentation9030201 - 21 Feb 2023
Cited by 13 | Viewed by 3222
Abstract
Phage ecology has attracted increasing attention in recent years. Fermented foods have rich and diverse microbial communities, which are not only the creators of the unique flavors in food, but also good hosts for bacteriophages. However, at present, much is known about the [...] Read more.
Phage ecology has attracted increasing attention in recent years. Fermented foods have rich and diverse microbial communities, which are not only the creators of the unique flavors in food, but also good hosts for bacteriophages. However, at present, much is known about the bacterial and fungal communities and their functions in fermented foods, but little is known about the bacteriophages that inhabit the bacteria. This article reviews recent findings on phage diversity in fermented foods, highlighting how these organisms influence and relate to the dynamics of microbial communities in fermented foods. The application of bacteriophages in fermented food is also discussed, which will help to better control the food fermentation process in the future and promote its further development by the food industry. Full article
(This article belongs to the Special Issue Perspectives on Microbial Ecology of Fermented Foods)
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