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Microorganisms in Fermented Food: Selection, Evaluation and Application

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

Deadline for manuscript submissions: closed (31 August 2025) | Viewed by 40105

Special Issue Editors


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Guest Editor
School of Food and Advanced Technology, Massey University, Auckland 0745, New Zealand
Interests: industrial microbiology; food safety and microbiology; development of starter cultures; indigenous food fermentations; lactic acid fermentations; sustainable food production systems
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Co-Guest Editor
ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Food Research Center, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
Interests: lactic acid bacteria; antimicrobials; bacteriocins; probiotics; antibiotic resistance; fermented food products
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The moment our ancestors unlocked the body’s ability to consume fermented foods, people found ways to transform raw materials into a variety of products with unique sensory characteristics and improved shelf life. Today, we can call several of those fermented foods, traditional. Fermentation is not just a way to preserve food; it is an integral part of our gastronomic identity. Migrations and settling in new regions contributed to the distribution of knowledge on the preparation of fermented foods. Consequently, fusions, traditions and innovations resulted in today’s large variety of fermented food products. The evolution of these products has been dependent on the type of raw materials available, the microorganisms responsible for the fermentation and the preparation methods used. Originally, spontaneous, uncontrolled fermentations occurred, and later the process of back-slopping was introduced. Empirical knowledge of the processes was passed on from one generation to another without much documentation. Therefore, the resultant food products had variable characteristics including safety. With the advent of modern food microbiology, microorganisms have been isolated from numerous traditional fermentations, characterised and developed into starter cultures used worldwide to produce high- and consistent-quality products using controlled fermentations. For over a century, starter cultures have been the subject of intensive research aimed at developing improved cultures with more predictable performance. From a scientific point of view, fermented food products are organically linked to the biological role of different microorganisms. Moreover, their role is not simply transforming raw materials to nutritional and gastronomic products; they play essential roles in bio-preservation and even serve as probiotics when consumed. The complex beneficial roles of microbes involved in the preparation of fermented food products deserve research focus and can be an inspiration for the creation of products with beneficial properties. Therefore, the demand for novel microbial cultures with predicted fermentation characteristics is ever increasing due to the demand for fermented products and beverages worldwide.

This Special Issue calls for the dissemination of research on the isolation, selection, characterisation and application of microbial fermentation cultures from a range of fermented products and beverages.

Prof. Dr. Anthony N. Mutukumira
Guest Editor

Dr. Svetoslav Todorov
Co-Guest Editor

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Keywords

  • mesophilic cultures
  • thermophilic cultures
  • single cultures
  • mixed cultures
  • characterisation
  • screening
  • traditional fermentation
  • indigenous fermentation
  • fermentation technology
  • precision fermentation
  • spontaneous fermentation

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Published Papers (3 papers)

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Review

17 pages, 1408 KB  
Review
Decoding the Microbial Diversity of Indian Fermented Foods: Integrating Ethnobiology, Multi-Omics and Functional Insights
by Priyanka Samantaray and Sudeshna Saha
Foods 2026, 15(4), 687; https://doi.org/10.3390/foods15040687 - 13 Feb 2026
Viewed by 1127
Abstract
India’s diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms—primarily lactic acid bacteria, yeasts, and molds—contribute functional properties that extend beyond food transformation to confer health [...] Read more.
India’s diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms—primarily lactic acid bacteria, yeasts, and molds—contribute functional properties that extend beyond food transformation to confer health benefits, including probiotic potential and metabolic regulation. This review integrates classical microbiological studies with modern molecular approaches such as metagenomics, metatranscriptomics, and metabolomics to elucidate the microbial diversity of Indian fermented foods. It highlights how geography, substrates, and ethnic traditions shape region-specific microbial consortia sustained through long-standing ethno-microbiological practices. Special focus is given to the glycemic modulation achieved through microbial fermentation, wherein organic acid production and resistant starch formation lower glycemic index and improve glucose metabolism. These processes, along with enhanced nutrient bioavailability, vitamin synthesis, and immunomodulation, illustrate the broader functional potential of fermentation. The review also examines interactions between food-borne microbes and the human gut microbiota, underscoring implications for personalized nutrition. Finally, it discusses modernization and commercialization strategies and outlines future directions involving multi-omics integration, indigenous starter cultures, and microbiome-based innovations to harness India’s microbial heritage for improved health and sustainable food development. Full article
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22 pages, 1455 KB  
Review
Kombucha: An Old Tradition into a New Concept of a Beneficial, Health-Promoting Beverage
by Dhuelly Kelly Almeida Andrade, Boying Wang, Emília Maria França Lima, Sergei Konstantinovich Shebeko, Alexey Mikhailovich Ermakov, Valentina Nikolaevna Khramova, Iskra Vitanova Ivanova, Ramon da Silva Rocha, Manuela Vaz-Velho, Anthony Nhamo Mutukumira and Svetoslav Dimitrov Todorov
Foods 2025, 14(9), 1547; https://doi.org/10.3390/foods14091547 - 28 Apr 2025
Cited by 29 | Viewed by 17188
Abstract
Kombucha is an ancient, fermented beverage that has gained increasing popularity worldwide due to its potential health benefits. Its origins trace back to China, from where it spread across Asia and Europe before reaching the modern global market. The fermentation of kombucha is [...] Read more.
Kombucha is an ancient, fermented beverage that has gained increasing popularity worldwide due to its potential health benefits. Its origins trace back to China, from where it spread across Asia and Europe before reaching the modern global market. The fermentation of kombucha is mediated by a Symbiotic Culture of Bacteria and Yeasts (SCOBY), comprising yeasts, acetic acid bacteria, and lactic acid bacteria. The microbial consortium plays a crucial role in the production of organic acids and bioactive metabolites, shaping the sensory characteristics of the beverage. Given the growing interest in kombucha as a functional beverage, this study aims to explore its historical background, fermentation process, and microbiological composition, including key yeasts, acid acetic bacteria, and lactic acid bacteria and their interactions. Additionally, we describe the potential health effects of kombucha, particularly its antimicrobial and antioxidant activity, the probiotic potential of the strains associated with kombucha, and safety considerations while also addressing the risks associated with its consumption. Although several studies suggested that kombucha may have antioxidants, antimicrobial, and probiotic properties, as well as contribute to gut microbiota regulation and immune system support, there is significant variability in the composition of the beverage, especially in artisanal preparations. This variability poses challenges in standardizing its potential effects and ensuring consistent safety. The risk of contamination further underscores the importance of adhering to strict sanitary production standards. To scientifically validate its health benefits and guarantee safe consumption, further research with larger sample sizes and robust methodologies is essential. The findings of this study will contribute to a deeper understanding of the functional properties of kombucha and provide scientific support for its safe and beneficial applications. Full article
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22 pages, 2174 KB  
Review
A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective
by Dong Han, Yunsong Yang, Zhantong Guo, Shuwen Dai, Mingchao Jiang, Yuanyuan Zhu, Yuqin Wang, Zhen Yu, Ke Wang, Chunchi Rong and Yongjian Yu
Foods 2024, 13(16), 2534; https://doi.org/10.3390/foods13162534 - 14 Aug 2024
Cited by 51 | Viewed by 20680
Abstract
In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa [...] Read more.
In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes. Full article
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