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Fermentation
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Yeast Biotechnology 4.0
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Yeast Biotechnology 4.0

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 December 2020) | Viewed by 43462

Special Issue Editor

Prof. Dr. Ronnie G. Willaert

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Guest Editor
Structural Biology Brussels Lab, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
Interests: yeast biotechnology; cell immobilization; beer brewing biochemistry and fermentation; mini- and microbioreactors; Saccharomyces cerevisiae; Candida; yeast space biology (bioreactors for microgravity research); yeast adhesins; yeast systems biology; glycobiology; nanobiotechnology; atomic force microscopy; protein crystallization; yeast protein structural biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used for the production of many interesting products, such as beer, wine, bread, biofuels and biopharmaceuticals. Saccharomyces cerevisiae (bakers’ yeast) is the yeast species that is surely the most exploited by man. Saccharomyces is a top choice organism for industrial applications, although its use for producing beer dates back to at least the 6th millennium BC. Bakers’ yeast has been a cornerstone of modern biotechnology, enabling the development of efficient production processes for antibiotics, biopharmaceuticals, technical enzymes, and ethanol and biofuels. Today, diverse yeast species are explored for industrial applications, such as e.g. Saccharomyces species, Pichia pastoris and other Pichia species, Kluyveromyces marxianus, Hansenula polymorpha, Yarrowia lipolytica, Candida species, Phaffia rhodozyma, wild yeasts for beer brewing, etc.

This Special Issue is focused on recent developments of yeast biotechnology with topics including recent techniques for characterizing yeast and their physiology (including omics and nanobiotechnology techniques), methods to adapt industrial strains (including metabolic, synthetic and evolutionary engineering) and the use of yeasts as microbial cell factories to produce biopharmaceuticals, enzymes, alcohols, organic acids, flavours and fine chemicals, and advances in yeast fermentation technology and industrial fermentation processes.

Topics including but not limited to:

Yeast characterization and analysis
Brewing yeasts (including wild yeasts), wine yeasts, baker’s yeasts.
Evolution and variation of genomes of industrial yeasts.
Yeast systems biology: genomics, proteomics, fluxomics, metabolomics, omics integration.
Yeast nanobiotechnology (nanoanalysis techniques, construction of nanostructures, etc.).

Yeast strain engineering
Yeast metabolic engineering: production of biofuels, secondary metabolites, commodity chemicals, proteins, biopharmaceuticals, material precursors.
Yeast synthetic biology: yeasts as cell factories, tools for controlling enzyme expression levels, strategies for regulating spatial localization of enzymes in yeast, regulatory networks, biomolecular logic gates.
Strain improvement via evolutionary engineering.

Fermentation technology
Industrial bioreactors.
Mini- and microbioreactors: single-cell analysis, high-throughput screening, microfluidic bioreactors.
Process intensification: high-density fermentations, high-gravity fermentation.
Fermentative stress adaptation.

Industrial fermentation processes
Production of food (bread, etc.) and beverages (beer, wine, cider, etc.).
Production of baker’s yeast.
Production of biofuels (bioethanol, 1-butanol, biodiesel, jetfuels), commodity chemicals, pharmaceuticals, material precursors, secondary metabolites.

Prof. Dr. Ronnie G. Willaert
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 2600 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.

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Published Papers (10 papers)

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Editorial

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4 pages, 201 KiB  
Editorial
Yeast Biotechnology 4.0
by Ronnie G. Willaert
Fermentation 2021, 7(2), 69; https://doi.org/10.3390/fermentation7020069 - 30 Apr 2021
Cited by 2 | Viewed by 2257
Abstract
This Special Issue is a continuation of the first, second, and third “Yeast Biotechnology” Special Issue series of the journal Fermentation (MDPI) [...] Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)

Research

Jump to: Editorial, Review

18 pages, 3596 KiB  
Article
Application of Autochthonous Yeast Saccharomyces cerevisiae XG3 in Treixadura Wines from D.O. Ribeiro (NW Spain): Effect on Wine Aroma
by Pilar Blanco, María Vázquez-Alén, Teresa Garde-Cerdán and Mar Vilanova
Fermentation 2021, 7(1), 31; https://doi.org/10.3390/fermentation7010031 - 25 Feb 2021
Cited by 5 | Viewed by 2545
Abstract
Yeast plays an essential role in winemaking. Saccharomyces cerevisiae strains involved in fermentation determine the chemical and sensory characteristics of wines. S. cerevisiae XG3, isolated in Galicia (NW Spain), has desirable oenological potential, which has been proved at a pilot scale to produce [...] Read more.
Yeast plays an essential role in winemaking. Saccharomyces cerevisiae strains involved in fermentation determine the chemical and sensory characteristics of wines. S. cerevisiae XG3, isolated in Galicia (NW Spain), has desirable oenological potential, which has been proved at a pilot scale to produce quality wines. This study applies XG3 as active dry yeast at an industrial scale for Treixadura wine elaboration, and compares it with commercial yeast and spontaneous fermentation within three wineries included in Denomination of Origin Ribeiro over two vintages. Fermentations are monitored using conventional methods, and microbiological implantation controls are carried out by mtDNA-RFLPs analysis. Wine basic chemical parameters are determined using OIV official methodology, and volatile aroma compounds are determined by GC-MS. Finally, wine sensory analysis is also performed. S. cerevisiae XG3 shows an acceptable implantation ability—as compared to commercial control strains. The wines from XG3 have a higher total acidity and lower alcohol content. Their volatile composition differs from control wines, since XG3 produces significantly higher concentrations of acetates, volatile acids, esters and volatile phenols, depending on the vintage and winery. However, lower differences are perceived at the sensory level, where fruity and floral descriptors are perceived by the panellists in XG3 wines. Therefore, XG3 constitutes an alternative to differentiate Treixadura wines. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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10 pages, 2068 KiB  
Article
Exploring the Impact of Lipid-Rich Food Industry Waste Carbon Sources on the Growth of Candida cylindracea DSM 2031
by Bartłomiej Zieniuk, Patrycja Mazurczak-Zieniuk and Agata Fabiszewska
Fermentation 2020, 6(4), 122; https://doi.org/10.3390/fermentation6040122 - 11 Dec 2020
Cited by 7 | Viewed by 2679
Abstract
The aim of this study was to evaluate the possibility of using several lipid-rich food industry wastes in the culture medium on the growth of Candida cylindracea DSM 2031 yeast strain. Four lipid wastes from the food industry: waste fish oil, rancid ghee, [...] Read more.
The aim of this study was to evaluate the possibility of using several lipid-rich food industry wastes in the culture medium on the growth of Candida cylindracea DSM 2031 yeast strain. Four lipid wastes from the food industry: waste fish oil, rancid ghee, waste pork lard, and waste duck processing oil were investigated. It has been shown in the laboratory scale that the above-mentioned wastes can be used to obtain biomass and produce lipolytic enzymes by the tested strain and the C. cylindracea extracellular lipase is not constitutive. High yields of biomass (12.84, 12.75, and 12.24 g/dm3) were obtained in media containing waste duck processing oil, olive oil, and waste pork lard, respectively. The highest lipolytic activity was obtained in the media containing waste fish oil and rancid ghee (0.050 and 0.047 U/cm3). During 192-h flask cultures the highest extracellular lipase activity and biomass yield were observed in the late logarithmic phase. The study showed that there is a potential for waste management to produce lipolytic enzymes or to produce yeast biomass. The use of waste substrates may contribute to lowering the costs of commercial production, and such a solution is part of the sustainable development strategy. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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12 pages, 264 KiB  
Article
Effects of Medium Components on Isocitric Acid Production by Yarrowia lipolytica Yeast
by Svetlana V. Kamzolova, Vladimir A. Samoilenko, Julia N. Lunina and Igor G. Morgunov
Fermentation 2020, 6(4), 112; https://doi.org/10.3390/fermentation6040112 - 20 Nov 2020
Cited by 9 | Viewed by 2349
Abstract
The microbiological production of isocitric acid (ICA) is more preferable for its application in medicine and food, because the resulting product contains only the natural isomer—threo-DS. The aim of the present work was to study ICA production by yeast using sunflower [...] Read more.
The microbiological production of isocitric acid (ICA) is more preferable for its application in medicine and food, because the resulting product contains only the natural isomer—threo-DS. The aim of the present work was to study ICA production by yeast using sunflower oil as carbon source. 30 taxonomically different yeast strains were assessed for their capability for ICA production, and Y. lipolytica VKM Y-2373 was selected as a promising producer. It was found that ICA production required: the limitation of Y. lipolytica growth by nitrogen, phosphorus, sulfur or magnesium, and an addition of iron, activating aconitate hydratase, a key enzyme of isocitrate synthesis. Another regulatory approach capable to shift acid formation to a predominant ICA synthesis is the use of inhibitors (itaconic and oxalic acids), which blocks the conversion of isocitrate at the level of isocitrate lyase. It is recommended to cultivate Y. lipolytica VKM Y-2373 under nitrogen deficiency conditions with addition of 1.5 mg/L iron and 30 mM itaconic acid. Such optimized nutrition medium provides 70.6 g/L ICA with a ratio between ICA and citric acid (CA) equal 4:1, a mass yield (YICA) of 1.25 g/g and volume productivity (QICA) of 1.19 g/L·h. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
14 pages, 16331 KiB  
Article
Snails as Taxis for a Large Yeast Biodiversity
by Madina Akan, Florian Michling, Katrin Matti, Sinje Krause, Judith Muno-Bender and Jürgen Wendland
Fermentation 2020, 6(3), 90; https://doi.org/10.3390/fermentation6030090 - 18 Sep 2020
Cited by 8 | Viewed by 3352
Abstract
Yeasts are unicellular fungi that harbour a large biodiversity of thousands of species, of which particularly ascomycetous yeasts are instrumental to human food and beverage production. There is already a large body of evidence showing that insects play an important role for yeast [...] Read more.
Yeasts are unicellular fungi that harbour a large biodiversity of thousands of species, of which particularly ascomycetous yeasts are instrumental to human food and beverage production. There is already a large body of evidence showing that insects play an important role for yeast ecology, for their dispersal to new habitats and for breeding and overwintering opportunities. Here, we sought to investigate a potential role of the terrestrial snails Cepaea hortensis and C. nemoralis, which in Europe are often found in association with human settlements and gardens, in yeast ecology. Surprisingly, even in a relatively limited culture-dependent sampling size of over 150 isolates, we found a variety of yeast genera, including species frequently isolated from grape must such as Hanseniaspora, Metschnikowia, Meyerozyma and Pichia in snail excrements. We typed the isolates using standard ITS-PCR-sequencing, sequenced the genomes of three non-conventional yeasts H. uvarum, Meyerozyma guilliermondii and P. kudriavzevii and characterized the fermentation performance of these three strains in grape must highlighting their potential to contribute to novel beverage fermentations. Aggravatingly, however, we also retrieved several human fungal pathogen isolates from snail excrements belonging to the Candida clade, namely Ca. glabrata and Ca. lusitaniae. Overall, our results indicate that diverse yeasts can utilise snails as taxis for dispersal. This courier service may be largely non-selective and thus depend on the diet available to the snails. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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17 pages, 1593 KiB  
Article
Saccharomyces cerevisiae Strain Diversity Associated with Spontaneous Fermentations in Organic Wineries from Galicia (NW Spain)
by David Castrillo, Noemi Neira and Pilar Blanco
Fermentation 2020, 6(3), 89; https://doi.org/10.3390/fermentation6030089 - 15 Sep 2020
Cited by 12 | Viewed by 2430
Abstract
Yeast play an essential role in wine quality. The dynamics of yeast strains during fermentation determine the final chemical and sensory characteristics of wines. This study aims to evaluate the Saccharomyces cerevisiae strains diversity in organic wineries from Galicia (NW Spain). Samples from [...] Read more.
Yeast play an essential role in wine quality. The dynamics of yeast strains during fermentation determine the final chemical and sensory characteristics of wines. This study aims to evaluate the Saccharomyces cerevisiae strains diversity in organic wineries from Galicia (NW Spain). Samples from spontaneous fermentations were taken in five wineries over three consecutive years (2013 to 2015). The samples were transported to the laboratory and processed following standard methodology for yeast isolation. S. cerevisiae strains were differentiated by mDNA-RFLPs. A total of 66 different strains were identified. Some of them presented a wide distribution and appeared in several wineries. However, other strains were typical from a specific winery. Similarity analysis using two different statistical tests showed significant differences in strain diversity among wineries. The results also revealed high biodiversity indexes; however, only some strains showed an important incidence in their distribution and frequency. Our findings confirmed that spontaneous fermentation favored the existence of a high S. cerevisiae strain diversity in organic wineries from Galicia. The presence of different yeasts during fermentation, specially winery-specific strains, contribute to increased wine complexity and differentiation. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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10 pages, 3233 KiB  
Article
Production of Proteins prM/M and E of Dengue Virus-3 in Pichia pastoris: Simplified Purification and Evaluation of Their Use as Antigens in Serological Diagnosis of Dengue
by Michelle D. O. Teixeira, Roberto S. Dias, John W. O. Prates, Juliana M. C. Monteiro, Mariana F. Xisto, Cynthia C. da Silva and Sérgio O. De Paula
Fermentation 2020, 6(3), 88; https://doi.org/10.3390/fermentation6030088 - 14 Sep 2020
Cited by 2 | Viewed by 2363
Abstract
Dengue is a major arbovirus affecting humans today. With the growing number of cases, it is essential to have large-scale production of antigens for the development of diagnostic kits for the rapid detection of patients infected by the virus and consequent proper medical [...] Read more.
Dengue is a major arbovirus affecting humans today. With the growing number of cases, it is essential to have large-scale production of antigens for the development of diagnostic kits for the rapid detection of patients infected by the virus and consequent proper medical intervention for them. In this work, we express the prM/M and E proteins of dengue virus-3 in yeast Pichia pastoris KM71H. The proteins were produced in soluble form in the supernatant of the culture and were purified by precipitation with ammonium sulfate. The fraction of 80% of ammonium sulfate was used as an antigen in an indirect enzyme-linked immunosorbent assay (ELISA), providing a sensitivity of 82.61% and a specificity of 89.25%. Thus, the methodology proposed here showed promise for obtaining antigens of dengue viruses and creating quick and inexpensive diagnostic tests, which is of great value since large portions of the areas affected by this disease are economically neglected. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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13 pages, 946 KiB  
Article
Selection of Wine Saccharomyces cerevisiae Strains and Their Screening for the Adsorption Activity of Pigments, Phenolics and Ochratoxin A
by Andrea Pulvirenti, Luciana De Vero, Giuseppe Blaiotta, Rossana Sidari, Giovanna Iosca, Maria Gullo and Andrea Caridi
Fermentation 2020, 6(3), 80; https://doi.org/10.3390/fermentation6030080 - 05 Aug 2020
Cited by 17 | Viewed by 2949
Abstract
Ochratoxin A is a dangerous mycotoxin present in wines and is considered the principal safety hazard in the winemaking process. Several authors have investigated the ochratoxin A adsorption ability of Saccharomyces cerevisiae yeasts, and specifically selected strains for this desired trait. In the [...] Read more.
Ochratoxin A is a dangerous mycotoxin present in wines and is considered the principal safety hazard in the winemaking process. Several authors have investigated the ochratoxin A adsorption ability of Saccharomyces cerevisiae yeasts, and specifically selected strains for this desired trait. In the present work, a huge selection of wine yeasts was done starting from Portuguese, Spanish and Italian fermenting musts of different cultivars. Firstly, 150 isolates were collected, and 99 non-redundant S. cerevisiae strains were identified. Then, the strains were screened following a multi-step approach in order to select those having primary oenological traits, mainly (a) good fermentation performance, (b) low production of H2S and (c) low production of acetic acid. The preselected strains were further investigated for their adsorption activity of pigments, phenolic compounds and ochratoxin A. Finally, 10 strains showed the desired features. The goal of this work was to select the strains capable of absorbing ochratoxin A but not pigments and phenolic compounds in order to improve and valorise both the quality and safety of red wines. The selected strains are considered good candidates for wine starters, moreover, they can be exploited to obtain a further enhancement of the specific adsorption/non-adsorption activity by applying a yeast breeding approach. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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Review

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16 pages, 825 KiB  
Review
Coffee and Yeasts: From Flavor to Biotechnology
by Lavinia Liliana Ruta and Ileana Cornelia Farcasanu
Fermentation 2021, 7(1), 9; https://doi.org/10.3390/fermentation7010009 - 07 Jan 2021
Cited by 33 | Viewed by 13934
Abstract
Coffee is one of the most consumed beverages in the world, and its popularity has prompted the necessity to constantly increase the variety and improve the characteristics of coffee as a general commodity. The popularity of coffee as a staple drink has also [...] Read more.
Coffee is one of the most consumed beverages in the world, and its popularity has prompted the necessity to constantly increase the variety and improve the characteristics of coffee as a general commodity. The popularity of coffee as a staple drink has also brought undesired side effects, since coffee production, processing and consumption are all accompanied by impressive quantities of coffee-related wastes which can be a threat to the environment. In this review, we integrated the main studies on fermentative yeasts used in coffee-related industries with emphasis on two different directions: (1) the role of yeast strains in the postharvest processing of coffee, the possibilities to use them as starting cultures for controlled fermentation and their impact on the sensorial quality of processed coffee, and (2) the potential to use yeasts to capitalize on coffee wastes—especially spent coffee grounds—in the form of eco-friendly biomass, biofuel or fine chemical production. Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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15 pages, 4452 KiB  
Review
An Overview of CRISPR-Based Technologies in Wine Yeasts to Improve Wine Flavor and Safety
by Alice Vilela
Fermentation 2021, 7(1), 5; https://doi.org/10.3390/fermentation7010005 - 02 Jan 2021
Cited by 15 | Viewed by 7177
Abstract
Modern industrial winemaking is based on the use of specific starters of wine strains. Commercial wine strains present several advantages over natural isolates, and it is their use that guarantees the stability and reproducibility of industrial winemaking technologies. For the highly competitive wine [...] Read more.
Modern industrial winemaking is based on the use of specific starters of wine strains. Commercial wine strains present several advantages over natural isolates, and it is their use that guarantees the stability and reproducibility of industrial winemaking technologies. For the highly competitive wine market with new demands for improved wine quality and wine safety, it has become increasingly critical to develop new yeast strains. In the last decades, new possibilities arose for creating upgraded wine yeasts in the laboratory, resulting in the development of strains with better fermentation abilities, able to improve the sensory quality of wines and produce wines targeted to specific consumers, considering their health and nutrition requirements. However, only two genetically modified (GM) wine yeast strains are officially registered and approved for commercial use. Compared with traditional genetic engineering methods, CRISPR/Cas9 is described as efficient, versatile, cheap, easy-to-use, and able to target multiple sites. This genetic engineering technique has been applied to Saccharomyces cerevisiae since 2013. In this review, we aimed to overview the use of CRISPR/Cas9 editing technique in wine yeasts to combine develop phenotypes able to increase flavor compounds in wine without the development of off-flavors and aiding in the creation of “safer wines.” Full article
(This article belongs to the Special Issue Yeast Biotechnology 4.0)
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