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Fermentation
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Microbial Ecosystems in Fermented Foods
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Microbial Ecosystems in 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: 30 June 2026 | Viewed by 5121

Special Issue Editors

Dr. Marija Milic

E-Mail Website
Guest Editor
Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
Interests: microbial fermentations; bioactive compounds determination in plant matrices; agro- waste bioconversion; microbiology; biotechnology
Dr. Katarina Mihajlovski

E-Mail Website
Guest Editor
Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
Interests: agro-waste bioconversion; fermentations; microbiology; biotechnology
Special Issues, Collections and Topics in MDPI journals
Dr. Snežana Dimitrijević

E-Mail Website
Guest Editor
Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
Interests: agro-waste bioconversion; fermentations; biotechnology

Special Issue Information

Dear Colleagues,

Fermented foods have long been celebrated not only for their unique flavors and extended shelf lives but also for their nutritional and health-promoting properties. Central to these benefits are the complex microbial ecosystems that drive fermentation processes. These dynamic communities—comprising bacteria, yeasts, molds—interact in intricate ways to transform raw ingredients into culturally significant and biologically active foods.

This Special Issue, Microbial Ecosystems in Fermented Foods, will deepen our understanding of microbial succession, resilience, and adaptation. From spontaneous fermentations shaped by local environments to controlled industrial processes, the contributions in this collection explore how specific microbial interactions influence product quality, safety, and bioactivity. This Special Issue will also highlight emerging technologies for monitoring and manipulating microbial communities, offering new pathways for innovation in food production.

For this Special Issue, I invite you to submit research articles and reviews on the effects of microbial ecosystems in fermentation and their technological applications, demonstrating their potential to reshape our food systems for a more sustainable future.

I hope this collection will inspire further interdisciplinary research and foster a greater appreciation of the invisible architects of fermented foods.

I look forward to receiving your contributions. 

Dr. Marija Milic
Dr. Katarina Mihajlovski
Dr. Snežana Dimitrijević
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 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

  • fermented foods
  • fermenting agents
  • microbial ecosystems
  • microbial succession
  • food quality
  • food safety
  • fermentation innovations
  • fermentation sustainability

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Published Papers (4 papers)

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Research

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20 pages, 804 KB  
Article
Exploring the Microbiota of Palm Wine, a Restricted Traditional Fermented Beverage from the Colombian Andes
by Johannes Delgado-Ospina, Carlos David Grande-Tovar, Maria del Pilar Garcia-Mendoza, Luis Gabriel Poveda-Perdomo, Fabián Felipe Fernández-Daza and Clemencia Chaves-López
Fermentation 2026, 12(5), 244; https://doi.org/10.3390/fermentation12050244 - 19 May 2026
Viewed by 605
Abstract
Colombian palm wine is a traditional fermented beverage produced from the sap of Attalea butyracea, whose microbiota and biochemical features remain poorly characterized. A comprehensive analytical framework was applied to palm wine samples from three Andean producers. This included the determination of [...] Read more.
Colombian palm wine is a traditional fermented beverage produced from the sap of Attalea butyracea, whose microbiota and biochemical features remain poorly characterized. A comprehensive analytical framework was applied to palm wine samples from three Andean producers. This included the determination of proximate composition, total phenolic content, and antioxidant activity, alongside a dual microbiological approach: traditional plate counting and high-throughput 16S rRNA/ITS metabarcoding. PICRUSt2 was employed to predict KEGG-based metabolic pathways to elucidate the microbial functional potential. The wines exhibited a low pH (3.35–3.65), a variable ethanol content (1.62–8.40 g/L), high residual sugars, moderate microbial loads, and limited antioxidant activity (as measured using the ABTS and DPPH assays). Analysis using high-throughput sequencing revealed high bacterial community diversity, dominated by Liquorilactobacillus nagelii, Limosilactobacillus fermentum, Limosilactobacillus panis, Lacticaseibacillus casei, and Zymomonas mobilis alongside the yeast Saccharomyces cerevisiae. Functional profiling revealed a significant enrichment in metabolic pathways related to carbohydrates, amino acids, and cofactors/vitamins, as well as xenobiotic biodegradation and metabolism. These findings provide the first integrated microbiological and physicochemical characterization of Colombian palm wine and highlight its biotechnological potential. Full article
(This article belongs to the Special Issue Microbial Ecosystems in Fermented Foods)
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20 pages, 1218 KB  
Article
Probiotic Fermentation: A Strategy to Induce the Significant Amplification of Phenolics and Bioactivity in Milk Thistle Seeds
by Suzana Dimitrijević-Branković, Valentina Nikšić, Milica Milutinović, Snežana Dimitrijević, Vladimir Filipović, Katarina Mihajlovski and Marija Milić
Fermentation 2026, 12(1), 26; https://doi.org/10.3390/fermentation12010026 - 3 Jan 2026
Viewed by 1197
Abstract
This study investigates how fermentation of milk thistle seeds (MTSs) by Saccharomyces cerevisiae var. boulardii, alone or with Lacticaseibacillus rhamnosus, affects phenolic compounds content and bioactivity of the resulting extracts. Microwave-assisted extraction parameters were optimized for maximal yield and validated for [...] Read more.
This study investigates how fermentation of milk thistle seeds (MTSs) by Saccharomyces cerevisiae var. boulardii, alone or with Lacticaseibacillus rhamnosus, affects phenolic compounds content and bioactivity of the resulting extracts. Microwave-assisted extraction parameters were optimized for maximal yield and validated for scale-up. The extracts were analyzed for total phenolic compounds (TPCs), total flavonoid compounds (TFCs), and bioactivities including antioxidant, antimicrobial, and prebiotic effects. Optimal extraction conditions were 70% ethanol, liquid to solid (L/S) ratio 30 mL/g, 180 W power, and 3 min duration, enabling energy-efficient recovery of antioxidants with higher yields than previously reported. Solid-state fermentation with S. boulardii significantly enhanced extraction efficiency, doubling TPC (647.6 ± 24.4 mg GAE/g dm) and TFC (87.04 ± 6.88 mg QE/g dm) contents, and antioxidant capacity (4.27 ± 0.19 mmol Fe2+/g dm) compared to non-fermented MTSs. Fermented extracts fully inhibited Staphylococcus aureus and partially Escherichia coli and Candida albicans. They also promoted the growth of probiotics such as S. boulardii and lactic acid bacteria strains, while non-fermented extracts showed opposite effects. These findings highlight the potential of MTS fermentation as a sustainable strategy to enhance bioactive compound yield and develop functional supplements that support human and animal health. Full article
(This article belongs to the Special Issue Microbial Ecosystems in Fermented Foods)
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21 pages, 1883 KB  
Article
Evolution of Brettanomyces bruxellensis During Secondary Fermentation of Sparkling Wines and Counteraction Strategies
by Raffaele Guzzon, Francesca Sicher, Tiziana Nardin, Mario Malacarne, Mauro Paolini and Roberto Larcher
Fermentation 2025, 11(11), 645; https://doi.org/10.3390/fermentation11110645 - 14 Nov 2025
Viewed by 1864
Abstract
The scope of this work is the study of the evolution of Brettanomyces bruxellensis, the main wine spoilage yeast, during bottle fermentation of sparkling wines. Lambrusco (Emilia, Italy) was considered as a model wine, for its high concentration of precursors for B. [...] Read more.
The scope of this work is the study of the evolution of Brettanomyces bruxellensis, the main wine spoilage yeast, during bottle fermentation of sparkling wines. Lambrusco (Emilia, Italy) was considered as a model wine, for its high concentration of precursors for B. bruxellensis activity, especially cinnamic acids. Five Lambrusco base wines furnished by a cooperative winery were inoculated with a 3-log concentration of B. bruxellensis and then underwent secondary fermentation in the bottle. Two strategies of contrast to B. bruxellensis, already successfully applied in red winemaking, were tested here for the first time in bottle fermentation: chitosan and a yeast proposed as a biocontrol agent. Bottle fermentation was monitored from a chemical and microbiological perspective. The resulting sparkling wines were analyzed by GC and HPLC–MS/MS to verify the presence of the key molecules indicating B. bruxellensis activity—biogenic amines, volatile phenols, and pyridines. Sensory analysis was also performed to establish the effects of the treatments on the overall wine profile. The results demonstrate that B. bruxellensis is capable of growing up to 5-log units, causing severe alterations of the wines, both from a chemical and sensorial point of view. The addition of chitosan at the beginning of bottle fermentation effectively mitigated the effects of B. bruxellensis, resulting in the wines being similar to the uncontaminated control. The effectiveness of the biocontrol agent under these conditions was lower and requires further investigation. Full article
(This article belongs to the Special Issue Microbial Ecosystems in Fermented Foods)
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Review

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12 pages, 251 KB  
Review
Microbial Ecology and Fermentation Dynamics of Moroccan Lben
by Sergi Maicas and Ismail Moukadiri
Fermentation 2026, 12(3), 142; https://doi.org/10.3390/fermentation12030142 - 6 Mar 2026
Viewed by 941
Abstract
Moroccan lben is a traditional spontaneously fermented milk widely consumed across the Maghreb. In this review, we synthesize data on spontaneously fermented milks from Morocco and the wider Maghreb–Middle Eastern region to infer the likely microbiota of Moroccan lben, with particular emphasis on [...] Read more.
Moroccan lben is a traditional spontaneously fermented milk widely consumed across the Maghreb. In this review, we synthesize data on spontaneously fermented milks from Morocco and the wider Maghreb–Middle Eastern region to infer the likely microbiota of Moroccan lben, with particular emphasis on dominant lactic acid bacteria such as Lactococcus lactis, Streptococcus thermophilus, Leuconostoc mesenteroides and lactobacilli sensu lato, alongside yeasts including Kluyveromyces marxianus and Saccharomyces cerevisiae. These communities drive a staged fermentation in which early mesophilic lactic acid bacteria (LAB) rapidly acidify the milk and initiate coagulation, intermediate heterofermentative LAB and yeasts generate key aroma compounds and mild effervescence, and late acid-tolerant lactobacilli contribute to flavor refinement and microbiological stability. We summarize how these bacteria and fungi collectively shape physicochemical, sensory and safety attributes through pH reduction, organic acid and bacteriocin production, proteolysis, and volatile formation, and discuss potential nutritional and health-related effects associated with bioactive peptides and putative probiotic strains. Finally, we identify major research gaps, including the need for high-resolution, culture-dependent and culture-independent studies, systematic safety assessments, and rational design of starter and adjunct cultures that reproduce traditional sensory profiles while improving process control. Full article
(This article belongs to the Special Issue Microbial Ecosystems in Fermented Foods)
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