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Fermentation
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Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses
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Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 5925

Special Issue Editor

Dr. Nicolas O. Soto-Cruz

E-Mail Website
Guest Editor
Tecnológico Nacional de México/IT Durango, Durango, México.
Interests: yeast physiology; yeast–yeast interactions; valorization of residues; volatile compound production; bioprocesses; mathematical modeling

Special Issue Information

Dear Colleagues,

The use of yeast fermentation, a technique almost as ancient as human civilization itself, has been instrumental in the production and preservation of food. Moreover, this practice has persisted to the present day. However, recent advances in understanding yeast fermentation have significantly expanded its application in various areas of human activity. Today, a deeper understanding of yeast physiology enables better control and performance of conventional fermentations, as well as designs of bioprocesses to produce valuable molecules across the food, cosmetic, pharmaceutical, and biofuel industries, among others.

This Special Issue will encompass a broad spectrum of original research and review papers. We welcome manuscripts on yeast fermentation and those focusing on the development of bioprocesses based on yeast cultures. Authors are invited to submit manuscripts on a diverse range of topics, including but not limited to the physiology of Saccharomyces and non-Saccharomyces yeasts, the isolation and characterization of new strains, yeast–yeast interactions, stress responses, omics in yeast research, strain development, obtaining hybrids, and the use of yeast to express heterologous genes.

Dr. Nicolas O. Soto-Cruz
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 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 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

  • antioxidants
  • bioconversion
  • biofuels
  • compounds for medical and health uses
  • fermented foods and beverages
  • food additives
  • volatile compounds
  • stress during yeast fermentation
  • yeast co-culture and sequential culture
  • yeast–yeast interactions

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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 (5 papers)

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Research

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14 pages, 1620 KiB  
Article
Transcriptional and Physiological Responses of Saccharomyces cerevisiae CZ to Octanoic Acid Stress
by Zhi-Hai Yu, Ming-Zhi Shi, Wen-Xuan Dong, Xiao-Zhu Liu, Wei-Yuan Tang and Ming-Zheng Huang
Fermentation 2025, 11(4), 180; https://doi.org/10.3390/fermentation11040180 - 1 Apr 2025
Viewed by 313
Abstract
This study elucidates the adaptive mechanisms of Saccharomyces cerevisiae CZ under octanoic acid stress, revealing concentration-dependent growth inhibition (76% lethality at 800 mg/L) and notable tolerance at 600 mg/L. Initial exposure (≤6 h) showed no growth impairment, but prolonged treatment induced dose-dependent lethality, [...] Read more.
This study elucidates the adaptive mechanisms of Saccharomyces cerevisiae CZ under octanoic acid stress, revealing concentration-dependent growth inhibition (76% lethality at 800 mg/L) and notable tolerance at 600 mg/L. Initial exposure (≤6 h) showed no growth impairment, but prolonged treatment induced dose-dependent lethality, accompanied by reduced H+/K+-ATPase activity and elevated malondialdehyde (MDA) levels, indicative of oxidative damage. Transcriptomic profiling of 5665 genes highlighted the predominant downregulation of ribosomal functions (translation, ribosome biogenesis) and amino acid metabolism pathways (e.g., ARO10, ARO9). Strain-specific regulatory dynamics were observed: (1) TPO1-mediated efflux was active at 400 mg/L but absent at 600 mg/L, suggesting compensatory mechanisms under high stress; (2) HTX1-related genes exhibited bidirectional regulation (downregulated at 400 mg/L vs. upregulated at 600 mg/L), reflecting metabolic flexibility; (3) ACC1 downregulation (600 mg/L) and unaltered SFK1 expression contrasted with lipid-remodeling strategies in engineered strains; and (4) PMA2 suppression diverged from literature-reported PMA1 activation, underscoring strain-specific energy reallocation. Suppression of ergosterol biosynthesis and ribosomal genes revealed a trade-off between stress adaptation and biosynthetic processes. These findings reconcile prior contradictions by attributing discrepancies to genetic backgrounds (CZ vs. laboratory/engineered strains) and methodological variations. Unlike strains relying on phospholipid asymmetry or oleic acid overproduction, CZ’s unique tolerance stems from integrated membrane homeostasis (via lipid balance) and metabolic conservation. This work emphasizes the critical role of strain-specific regulatory networks in octanoic acid resistance and provides insights for optimizing yeast robustness through targeted engineering of membrane stability and metabolic adaptability. Future studies should employ multi-omics integration to unravel the dynamic gene regulatory logic underlying these adaptive traits. Full article
(This article belongs to the Special Issue Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses)
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15 pages, 943 KiB  
Article
Tolerance of Kluyveromyces marxianus Under Acetic Acid-, Isoamyl Alcohol-, Hydrogen Peroxide-, and Ethanol-Induced Stress
by Cesia K. Acosta-Cuevas, Jesús B. Páez-Lerma, Juan A. Rojas-Contreras, Lucio Rodríguez-Sifuentes, Ana K. Sánchez-Castañeda and Nicolas O. Soto-Cruz
Fermentation 2025, 11(4), 171; https://doi.org/10.3390/fermentation11040171 - 25 Mar 2025
Viewed by 513
Abstract
Kluyveromyces marxianus is a yeast that can be used as a microbial factory. However, little is known about its response to stress conditions. This work evaluated the response of this yeast against ethanol, acetic acid, isoamyl alcohol, and hydrogen peroxide as stress agents. [...] Read more.
Kluyveromyces marxianus is a yeast that can be used as a microbial factory. However, little is known about its response to stress conditions. This work evaluated the response of this yeast against ethanol, acetic acid, isoamyl alcohol, and hydrogen peroxide as stress agents. Cytotoxicity assays were performed to assess the residual viability using a direct method (CFU counting) and an indirect method based on the reduction in MTT. Then, fermentation kinetics were performed at IC30 and IC50 for each stress factor to evaluate the effect of moderate and intense stress. This work is the first report presenting IC50 values for ethanol (21.82 g/L), acetic acid (1.19 g/L), isoamyl alcohol (2.74 g/L), and hydrogen peroxide (0.09 g/L) in K. marxianus. The IC50 values for the indirect method are between 3.7 and 68% higher than those for the direct method. Hydrogen peroxide and ethanol were the stress agents showing the highest overestimations. The results presented here demonstrated the overestimation of cell viability by the indirect method. Direct CFU counting is an adequate method to determine yeast viability during toxicity studies of chemical compounds. It was also established that ethanol and hydrogen peroxide have the highest toxicity against K. marxianus ITD-01005 during fermentation at concentrations equivalent to IC30 and IC50 of each stress agent. Full article
(This article belongs to the Special Issue Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses)
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11 pages, 3837 KiB  
Article
Carnosic Acid Production from Sugarcane Syrup by Engineered Yeast in Fed-Batch Fermentation
by Erdem Carsanba, Sara Fernandes, Felipe Beato, Luís Carlos Carvalho, Ana Pintado, Ana Lopes, Mónica Ribeiro, Tânia Leal, Manuela Pintado and Carla Oliveira
Fermentation 2025, 11(3), 147; https://doi.org/10.3390/fermentation11030147 - 15 Mar 2025
Viewed by 565
Abstract
Phenolic diterpene carnosic acid (CA) is widely used in the food, nutritional health, and cosmetic industries due to its antioxidative and antimicrobial properties. This work aimed to overproduce CA in Saccharomyces cerevisiae from sugarcane syrup in fed-batch 2 L bioreactor fermentation. A geranylgeranyl [...] Read more.
Phenolic diterpene carnosic acid (CA) is widely used in the food, nutritional health, and cosmetic industries due to its antioxidative and antimicrobial properties. This work aimed to overproduce CA in Saccharomyces cerevisiae from sugarcane syrup in fed-batch 2 L bioreactor fermentation. A geranylgeranyl diphosphate (GGPP)-producing strain modified with genes encoding the enzymes copalyl diphosphate synthase (Pv.CPS), miltiradiene synthase (Ro.KSL2), hydroxy ferruginol synthase (Ro.HFS), CA synthase (Ro.CYP76AK8), CYP reductase (At.ATR1), and transketolase (TKL1) was used. Lowering the feed rate from 12–26 g/L/h to 7–8 g/L/h, and the use of a dynamic dissolved oxygen (DO) trigger (min. 10%, max. 40%, threshold 70%) instead of a DO trigger of 30%, enhanced CA production by 27%. As a result, the highest CA titer ever reported to date, 191.4 mg/L, was obtained in 4-day fermentation. This study shows the feasibility of engineered yeast to produce CA from the sustainable feedstock sugarcane syrup. Full article
(This article belongs to the Special Issue Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses)
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12 pages, 3752 KiB  
Article
Transcriptomic Analysis of Cell Stress Response in Wickerhamomyces anomalus H4 Under Octanoic Acid Stress
by Zhi-Hai Yu, Li Li, Qiu-Yu Chen, Bing-Xuan Huang, Ming-Zhi Shi, Wan-Jin Dong, Yuan Zu, Ming-Zheng Huang and Xiao-Zhu Liu
Fermentation 2024, 10(11), 563; https://doi.org/10.3390/fermentation10110563 - 4 Nov 2024
Viewed by 1318
Abstract
The purified yeast strain H4, identified as W. anomalus through morphological, genetic, and phylogenetic analyses, was characterized and compared to a commercial Saccharomyces cerevisiae strain X16. W. anomalus H4 exhibited distinct morphological features. It demonstrated notable tolerance to 11% ethanol, 220 g/L glucose, [...] Read more.
The purified yeast strain H4, identified as W. anomalus through morphological, genetic, and phylogenetic analyses, was characterized and compared to a commercial Saccharomyces cerevisiae strain X16. W. anomalus H4 exhibited distinct morphological features. It demonstrated notable tolerance to 11% ethanol, 220 g/L glucose, and 200 mg/L octanoic acid, similar to X16, except for having a lower tolerance to SO2. Survival analysis under various stress conditions revealed that ethanol and octanoic acid had the most detrimental effects, with 56% cell mortality at 13% ethanol and 400 mg/L octanoic acid. Transcriptomic analysis under octanoic acid stress showed that at 200 mg/L, 3369 differentially expressed genes (DEGs) were induced, with 1609 being upregulated and 1760 downregulated, indicating broad transcriptional reprogramming. At 400 mg/L, only 130 DEGs were detected, suggesting a more limited response. KEGG pathway analysis indicated that most DEGs at 200 mg/L were associated with the “ribosome” and “proteasome” pathways, reflecting disruptions in protein synthesis and turnover. At 400 mg/L, the DEGs were primarily related to “DNA replication” and “pyruvate metabolism”. These findings highlight the adaptive mechanisms of W. anomalus H4 to environmental stresses, particularly octanoic acid, and its potential for use in brewing and fermentation processes. Full article
(This article belongs to the Special Issue Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses)
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Review

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24 pages, 419 KiB  
Review
Continuous Cultivation of Yarrowia lipolytica: Potential, Challenges, and Case Studies
by Svetlana V. Kamzolova
Fermentation 2024, 10(12), 619; https://doi.org/10.3390/fermentation10120619 - 3 Dec 2024
Viewed by 2178
Abstract
Currently, the yeast Yarrowia lipolytica is regarded as one of the most promising producers of protein, lipids, polyols, organic acids, and other metabolites. The objective of enhancing the efficiency of the target product biosynthesis can be achieved through the improvement of the strains-producers [...] Read more.
Currently, the yeast Yarrowia lipolytica is regarded as one of the most promising producers of protein, lipids, polyols, organic acids, and other metabolites. The objective of enhancing the efficiency of the target product biosynthesis can be achieved through the improvement of the strains-producers and the optimization of the cultivation conditions. The present review assesses the potential of continuous cultivation methods (chemostat, turbidostat, pH-auxostat, changestats, etc.) in order to gain insight into the impact of strains and cultivation conditions on the productivity of the developed bioprocesses. The utilization of continuous cultivation methods enables the implementation of processes under controlled and reproducible conditions, thus stabilizing the parameters of the cultivation and the physiological state of the producer, and obtaining homogeneous samples. The review focuses on nitrogen-limited chemostat cultures, which represent the most commonly employed strategy for investigating the physiological and biochemical characteristics of the yeast Y. lipolytica and for developing the processes for the production of lipids, erythritol, citric acid, and recombinant proteins. To date, such an analysis of the literature has not been conducted in the context of the yeast Y. lipolytica. Full article
(This article belongs to the Special Issue Current Research in Yeast Fermentation: Physiology, Biotechnology, and Bioprocesses)
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