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Fermentation
Special Issues
Yeasts as Microbial Cell Factories: Diversity, Biotechnology Potential and Applications
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Yeasts as Microbial Cell Factories: Diversity, Biotechnology Potential and Applications

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Yeast".

Deadline for manuscript submissions: 15 July 2026 | Viewed by 2949

Special Issue Editor

Dr. Anna Maria Kot

E-Mail Website
Guest Editor
Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences, Warsaw, Poland
Interests: food biotechnology; microbial isolation; microbial lipid biosynthesis; carotenoids produced by yeasts; biotechnological valorization of industrial waste

Special Issue Information

Dear Colleagues,

Yeasts are metabolically versatile microorganisms that are of great relevance for industrial biotechnology and, beyond their traditional roles in food and beverage fermentation, both conventional and non-conventional yeasts are increasingly recognized as efficient microbial cell factories for the production of high-value compounds such as lipids, carotenoids, enzymes, organic acids, and bioethanol.

This Special Issue aims to highlight recent advances in yeast biodiversity, functional properties, metabolic engineering, and bioprocess optimization, and topics of interest include the discovery of novel yeast species, the probiotic potential of yeasts, their interactions in co-cultivation systems, their applications in food and health sectors, and the sustainable biotechnological use of industrial residues. Both original research and review articles are welcome.

Dr. Anna Maria Kot
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

  • yeast biodiversity
  • non-conventional yeasts
  • fermentation
  • functional metabolites
  • food biotechnology
  • microbial waste valorization
  • bioprocess optimization

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Published Papers (3 papers)

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Research

15 pages, 1227 KB  
Article
Development of Probiotic Dark Chocolate Enriched with Encapsulated Saccharomyces boulardii: Storage Stability and In Vitro Gastrointestinal Survival
by Eda Kılıç Kanak and Suzan Öztürk Yılmaz
Fermentation 2026, 12(3), 145; https://doi.org/10.3390/fermentation12030145 - 11 Mar 2026
Viewed by 476
Abstract
This study investigated the development of a sugar-free prebiotic and probiotic dark chocolate formulated with 39.76% cocoa mass, 41.856% cocoa butter, 14.8% inulin, and 1.6% stevioside. To enhance the stability of the probiotic yeast Saccharomyces boulardii, a microencapsulation technique using a cocoa [...] Read more.
This study investigated the development of a sugar-free prebiotic and probiotic dark chocolate formulated with 39.76% cocoa mass, 41.856% cocoa butter, 14.8% inulin, and 1.6% stevioside. To enhance the stability of the probiotic yeast Saccharomyces boulardii, a microencapsulation technique using a cocoa powder, Na-alginate, and fructooligosaccharides (10:1:1 ratio) matrix was employed. The physicochemical properties and probiotic viability were monitored over a 120-day storage period at 25 °C. A significant increase in pH values was observed during storage (p < 0.05), while water activity (aw) values significantly decreased (p < 0.05). Encapsulation provided superior protection, with encapsulated samples retaining 2.51 log CFU/g more probiotics than unencapsulated samples after 120 days. Furthermore, in vitro gastrointestinal digestion assays conducted after one day of storage demonstrated the protective efficacy of the matrix; while unencapsulated probiotics suffered a drastic reduction of 6.42 log CFU/g under gastric conditions (pH 3, 2 h), the encapsulated probiotics showed a significantly lower reduction of only 3.99 log CFU/g. These results confirm that the Na-alginate/FOS-based encapsulation significantly improves the resilience of S. boulardii against both storage conditions and gastrointestinal stress, making this sugar-free prebiotic chocolate an effective delivery vehicle for probiotic yeasts. Full article
(This article belongs to the Special Issue Yeasts as Microbial Cell Factories: Diversity, Biotechnology Potential and Applications)
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18 pages, 7100 KB  
Article
Intraspecific Diversity of Saccharomyces cerevisiae Associated with Traditional Fermented Beverages in Chiapas, Mexico
by Maritza Tawas-Penagos, Ruth Percino-Daniel, José Alberto Narváez-Zapata, René Quezada-Romero, Anne Christine Gschaedler-Mathis and Alma Gabriela Verdugo-Valdez
Fermentation 2025, 11(12), 697; https://doi.org/10.3390/fermentation11120697 - 16 Dec 2025
Viewed by 613
Abstract
Traditional fermented beverages from Chiapas, Mexico, represent an important source of microbial diversity, particularly of Saccharomyces cerevisiae. In native strains isolated from traditional fermented beverages, Saccharomyces cerevisiae has been observed to display distinct morphological and physiological traits; therefore, the aim of this [...] Read more.
Traditional fermented beverages from Chiapas, Mexico, represent an important source of microbial diversity, particularly of Saccharomyces cerevisiae. In native strains isolated from traditional fermented beverages, Saccharomyces cerevisiae has been observed to display distinct morphological and physiological traits; therefore, the aim of this study was to evaluate the population growth and the tolerance of twenty isolates to different stress factors such as temperature, osmotic pressure, and high ethanol concentrations, as well as the genetic variability through interdelta analysis, and to determine whether these physiological and molecular characteristics are associated with the type of beverage and the locality of origin. Differences were observed in tolerance to various factors, including high ethanol concentrations and elevated temperatures, as well as in the production of volatile compounds, with Taberna and Mezcal isolates showing notable performance. These isolates were able to withstand temperatures ranging from 43 to 45 °C and ethanol concentrations of up to 17% in Mezcal and Pox isolates, and 15% in Taberna isolates. High concentrations of isoamyl acetate and higher alcohols such as isoamyl alcohol were detected. In addition, the genetic variability of the isolates was evaluated, and its relationship with the type of beverage and the geographical origin of production was explored, including isolates obtained from Taberna, Mezcal, Pox, and Chicha de Chilacayote. Intraspecific variability was assessed through a retrotransposon-based analysis of the interdelta region using different primer combinations (δ1-δ2, δ12-δ21, and δ12-δ2). The generated banding patterns were analyzed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), which enabled the identification of molecular variability patterns among the isolates. Furthermore, a UPGMA analysis was performed using physiological and compound production data, revealing a relationship between these characteristics and the geographical origin of the isolates. The results revealed a high degree of intraspecific variability, which was associated with both the type of beverage and the locality of origin of the isolates. Full article
(This article belongs to the Special Issue Yeasts as Microbial Cell Factories: Diversity, Biotechnology Potential and Applications)
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20 pages, 1067 KB  
Article
A Potential of Agro-Industrial Biowaste as Low-Cost Substrates for Carotenoid Production by Rhodotorula mucilaginosa
by Olja Šovljanski, Dragoljub Cvetković, Tara Budimac, Anja Vučetić, Ana Tomić, Teodora Marić and Aleksandra Ranitović
Fermentation 2025, 11(9), 531; https://doi.org/10.3390/fermentation11090531 - 12 Sep 2025
Cited by 1 | Viewed by 1463
Abstract
The sustainable production of natural pigments is gaining attention as industries seek alternatives to synthetic additives. This study explored agro-industrial biowastes as feedstocks for carotenoid biosynthesis by Rhodotorula mucilaginosa (natural isolate from Jerusalem artichoke), aiming to identify an optimal substrate that combines high [...] Read more.
The sustainable production of natural pigments is gaining attention as industries seek alternatives to synthetic additives. This study explored agro-industrial biowastes as feedstocks for carotenoid biosynthesis by Rhodotorula mucilaginosa (natural isolate from Jerusalem artichoke), aiming to identify an optimal substrate that combines high productivity with economic and environmental feasibility. Thirteen biowastes, including grape pomace, crude glycerol, chicken feathers, sugar beet juice, and pea protein isolate, were systematically evaluated for their impact on yeast growth and pigment accumulation. Carotenoid yields ranged from 21.4 to 187.2 mg/100 g dry weight, with the highest volumetric productivity achieved in pea protein isolate (14.98 mg/L), untreated white grape pomace (14.09 mg/L), and crude glycerol (13.87 mg/L). To assess scalability, a simplified techno-economic and sustainability analysis was applied, revealing that although pea protein isolate offered the best yields, its high market cost limited industrial feasibility. In contrast, untreated grape pomace and crude glycerol emerged as low-cost, abundant alternatives with strong circular bioeconomy potential. Fed-batch bioreactor validation using untreated grape pomace confirmed its suitability, achieving a 43% improvement in carotenoid productivity (20.1 mg/L) compared to shake-flask trials. These results position untreated grape pomace as the optimal substrate–strategy combination for sustainable carotenoid production linking agro-waste valorization with high-value bioproduct generation. This study provides both experimental evidence and economic rationale for integrating winery residues into industrial pigment production chains, advancing yeast biotechnology toward more circular and resource-efficient models. Full article
(This article belongs to the Special Issue Yeasts as Microbial Cell Factories: Diversity, Biotechnology Potential and Applications)
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