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Fermentation
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Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and...
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Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses

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

Deadline for manuscript submissions: 31 May 2026 | Viewed by 12900

Special Issue Editor

Dr. Karina Teixeira Magalhães-Guedes

E-Mail Website
Guest Editor
Department of Bromatological Analysis, Pharmacy Faculty, Federal University of Bahia, Salvador, Brazil
Interests: food; clinical; medical and environmental microbiology; microbial biotechnology; probiotic and psychobiotic microorganisms; biotechnology of new products/supplements for human health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to highlight cutting-edge research on the use of microorganisms—including bacteria, yeasts, filamentous fungi, and microalgae—in bioprocesses and biotechnological applications with relevance to the food, environmental, and health sectors involving fermentative processes.

We welcome original research articles and reviews that explore, but are not limited to, the following themes:

  • Probiotic biotechnology and functional microbial strains for food and health applications;
  • Genetically engineered microorganisms in fermentation processes;
  • Microbial transformation and valorization of agro-industrial by-products;
  • Applications of microbial fermentation in health-related bioprocesses, such as postbiotic or metabolite production;
  • Microbial consortia and synthetic biology for sustainable bioprocesses;
  • Environmental biotechnology using microbial systems for bioremediation and waste valorization.

This Special Issue intends to bring together interdisciplinary research that bridges microbiology, biotechnology, process engineering, and sustainable development goals (SDGs), aiming to foster innovation in both academic and industrial settings.

Dr. Karina Teixeira Magalhães-Guedes
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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 2100 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

  • environmental biotechnology
  • functional foods
  • genetically engineered microorganisms
  • microbial fermentation
  • postbiotics and microbial metabolites
  • probiotic biotechnology
  • sustainable bioprocesses
  • synthetic biology and microbial consortia
  • valorization of agro-industrial by-products

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  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
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Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

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Research

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17 pages, 3090 KB  
Article
Cupuassu (Theobroma grandiflorum) as a Functional Ingredient in Fermented Cow’s Milk: Technological, Sensory, Nutritional, and Microbiological Viability
by Yasmin Ourives Domingues, Andrea Pissatto Peres, Rafael Alexandre dos Santos Martins, Ana Rosa de Souza Silva, Cláudia Puerari, Juliana Aparecida Correia Bento and Maressa Caldeira Morzelle
Fermentation 2026, 12(1), 20; https://doi.org/10.3390/fermentation12010020 - 31 Dec 2025
Viewed by 923
Abstract
The incorporation of native Amazonian fruits into dairy products has increased due to their ability to improve technological, sensory, nutritional, and biological properties. Therefore, this study aimed to evaluate the impact of cupuassu (Theobroma grandiflorum) pulp on the chemical, physical, and [...] Read more.
The incorporation of native Amazonian fruits into dairy products has increased due to their ability to improve technological, sensory, nutritional, and biological properties. Therefore, this study aimed to evaluate the impact of cupuassu (Theobroma grandiflorum) pulp on the chemical, physical, and sensory characteristics of fermented milk, using a central rotational composite design with two factors (sugar and cupuassu pulp). Our results are presented as response surfaces, showing that cupuassu pulp is positively associated with the examined parameters (pH, titratable acidity, total soluble solids, total phenolic compounds, syneresis, and water retention capacity). The analysis suggested a promising formulation containing 27.8% cupuassu pulp and 8.6% sugar. The pulp and this promising formulation were characterized by pH, titratable acidity, total soluble solids, proximate composition, and bioactive compounds (total phenolic compounds (TPC) and antioxidant activity). The physicochemical stability of the beverage was monitored over 28 days. Sensory acceptance and purchase intention for the promising formulation were also evaluated. Cupuassu contributed to an increase in soluble solids, while pH and titratable acidity remained stable during storage. Additionally, cupuassu pulp increased the total phenolic content and enhanced the beverage’s antioxidant activity. Sensory analysis showed that adding cupuassu pulp positively influenced all evaluated attributes (83% acceptance) and was associated with a favorable purchase intention. Incorporating cupuassu pulp into fermented milk proved to be technologically feasible and sensorially acceptable, meeting the demand for innovative dairy beverages with functional and sensory benefits. Full article
(This article belongs to the Special Issue Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses)
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13 pages, 1033 KB  
Article
Nutritional and Physicochemical Attributes of Sourdough Breads Fermented with a Novel Pediococcus acidilactici ORE 5 Strain
by Ioanna Mantzourani, Athanasios Alexopoulos, Gregoria Mitropoulou, Yiannis Kourkoutas and Stavros Plessas
Fermentation 2025, 11(12), 666; https://doi.org/10.3390/fermentation11120666 - 28 Nov 2025
Cited by 2 | Viewed by 1445
Abstract
This study evaluated the application of Pediococcus acidilactici ORE 5 (applied in free or immobilized form in a prebiotic matrix called “trahanas”) in sourdough bread production. Specific volumes of all the produced bread samples varied at approximately the same levels (2.50 to 2.54 [...] Read more.
This study evaluated the application of Pediococcus acidilactici ORE 5 (applied in free or immobilized form in a prebiotic matrix called “trahanas”) in sourdough bread production. Specific volumes of all the produced bread samples varied at approximately the same levels (2.50 to 2.54 mL/g), indicating a satisfactory dough expansion. In contrast, acidity differed significantly (p < 0.05). Sourdough bread produced with immobilized cells (IB) exhibited the lowest pH (4.30) and the highest titratable acidity (9.13 mL NaOH N/10), followed by the sourdough bread produced with free cells (FB) and the control bread (CB), reflecting the enhanced metabolic activity of immobilized cells supported by the prebiotic matrix. The organic acid analysis revealed higher levels of lactic (2.96 g/kg) and acetic acid (0.99 g/kg) in the IB sample, along with increased minor acids. The high organic acid content contributed to a delayed rope (14.7 days) and mold spoilage (7.3 days) compared to the CB sample, enhancing microbial stability. In addition, the nutritional properties of the produced sourdough breads containing P. acidilactici ORE 5 were improved significantly. The IB sample demonstrated the highest total phenolic content (85 mg GAE/100 g), followed by the FB sample (61 mg/100 g) and the CB sample (48 mg/100 g), while phytic acid levels were markedly reduced (93% in IB and 80% in FB). A sensory evaluation confirmed the maintained overall acceptability, with enhanced flavor scores for sourdough breads containing P. acidilactici ORE 5. These findings indicate that P. acidilactici ORE 5, particularly in immobilized form, could be an effective functional starter culture for sourdough bread, highlighting its potential for applications in functional bakery products. Full article
(This article belongs to the Special Issue Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses)
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18 pages, 1090 KB  
Article
Enhancing Soy Yogurt with Microencapsulated Limosilactobacillus reuteri: Viability and Sensory Acceptability
by Ricardo H. Hernández-Figueroa, Yani D. Ramírez, Aurelio López-Malo and Emma Mani-López
Fermentation 2025, 11(8), 423; https://doi.org/10.3390/fermentation11080423 - 22 Jul 2025
Cited by 1 | Viewed by 2893
Abstract
This study aimed to microencapsulate Limosilactobacillus reuteri DSM 17938 to enrich soy yogurt flavored with peach jam. The effect of three concentrations of alginate and coating chitosan were evaluated in terms of probiotic viability, and the physicochemical and sensory properties of soy yogurt. [...] Read more.
This study aimed to microencapsulate Limosilactobacillus reuteri DSM 17938 to enrich soy yogurt flavored with peach jam. The effect of three concentrations of alginate and coating chitosan were evaluated in terms of probiotic viability, and the physicochemical and sensory properties of soy yogurt. Lim. reuteri was microencapsulated in alginate (1, 2, and 3%) and coated with chitosan (0, 0.4, and 0.8%). Soymilk was fermented using Lactobacillus bulgaricus and Streptococcus thermophilus. Soy yogurt was combined with probiotic beads and peach jam and stored for 27 days at 4 °C. The pH, titratable acidity, and probiotic viability of probiotic peach soy yogurt (PPSY) were determined during storage. Alginate at 3% and alginate (2%) coated with 0.4% chitosan maintained probiotic counts at 8 and 7.5 log CFU/g after 27 days. The pH of PPSY decreases rapidly and drastically during storage when probiotic-free cells are added. The PPSY containing alginate (3%) beads, alginate (2%) coated with chitosan (0.4%), and probiotic-free cells had a similar level of acceptance in color, texture, and odor (p > 0.05), while flavor and overall acceptability were significantly higher (p < 0.05) in PPSY with probiotic beads. These findings support the use of microencapsulation strategies in developing functional plant-based probiotic foods. Full article
(This article belongs to the Special Issue Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses)
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Review

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20 pages, 1645 KB  
Review
Smart and Functional Probiotic Microorganisms: Emerging Roles in Health-Oriented Fermentation
by Karina Teixeira Magalhães, Raquel Nunes Almeida da Silva, Adriana Silva Borges, Ana Elisa Barbosa Siqueira, Claudia Puerari and Juliana Aparecida Correia Bento
Fermentation 2025, 11(9), 537; https://doi.org/10.3390/fermentation11090537 - 16 Sep 2025
Cited by 11 | Viewed by 7023
Abstract
The incorporation of probiotic microorganisms into fermented foods has long been recognized as a promising strategy to enhance gut health and overall well-being. Conventional probiotics, mainly from the bacterial genera Lactobacillus, Bifidobacterium, Lacticaseibacillus, Levilactobacillus, Lactiplantibacillus and yeast genus Saccharomyces [...] Read more.
The incorporation of probiotic microorganisms into fermented foods has long been recognized as a promising strategy to enhance gut health and overall well-being. Conventional probiotics, mainly from the bacterial genera Lactobacillus, Bifidobacterium, Lacticaseibacillus, Levilactobacillus, Lactiplantibacillus and yeast genus Saccharomyces, contribute to gastrointestinal homeostasis, immune modulation, and metabolic balance. Building on these foundations, recent advances in synthetic biology, systems microbiology, and genetic engineering have enabled the development of smart probiotics: engineered or selectively enhanced strains capable of sensing environmental cues and producing targeted bioactive compounds, such as neurotransmitters and anti-inflammatory peptides. These next-generation microorganisms offer precision functionality in food matrices and hold promise for applications in gastrointestinal health, immune support, and gut–brain axis modulation. However, their deployment also raises critical questions regarding biosafety, regulatory approval, and consumer acceptance. This review provides a comprehensive overview of the mechanisms of action, biotechnological strategies, and health-oriented fermentation applications of smart and functional probiotics, emphasizing their role in the future of personalized and evidence-based functional foods. Full article
(This article belongs to the Special Issue Emerging Microbial Technologies in Fermentation: Innovations in Food, Environmental, and Health Bioprocesses)
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