Leveraging Yeast Biodiversity for Biotechnology

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Evolution, Biodiversity and Systematics".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 40270

Special Issue Editors


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Guest Editor
ISVV/Bordeaux Sciences Agro, Unité de Recherche Œnologie, EA 4577, INRAE 1366, Villenave d’Ornon, France
Interests: wine yeast; genetic and phenotypic diversity; non-conventional yeasts; fermentation; yeast selection

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Guest Editor
INRAE, Sciences pour l’oenologie (SPO), 34060 Montpellier, France
Interests: comparative genomics of yeasts; population genomics; biodiversity of yeast in natural and anthropic environments; functional genomics; genetic engineering; biotechnology

Special Issue Information

Dear colleagues, 

Yeasts are widespread in natural and anthropic environments where they play crucial ecological roles. Taking advantage of their metabolic capabilities, yeasts have been exploited for a long time, for thousands of years, initially for the production of beverages and fermented foods such as wine, beer, and bread. With the advent of the biotechnology era, yeasts have been used as cell factories to produce enzymes, pharmaceutical proteins, synthons for the oleochemistry, etc. Chassis for white biotechnology or starters for industrial fermented foods and beverages have been optimized from a limited number of genetic backgrounds. However, today, significant advances in biodiversity knowledge have opened the way to leveraging unknown strains or species for biotechnological innovation. This Special Issue of the Journal of Fungi will focus on different ways of biodiversity exploitation to promote innovative applications in biotechnology: alternative models, selection, or creation of new species and strains making use of genetic engineering, population genomics, QTL, or phenotyping. Topics related to the impact of humans, domestication, and adaptation will also be considered.

Prof. Dr. Isabelle Masneuf-Pomarede
Dr. Cécile Neuvéglise
Guest Editors

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Keywords

  • biodiversity
  • biotechnology
  • metabolic engineering
  • population genomics
  • QTL
  • genetic
  • genomic and phenotypic diversity
  • non-conventional yeast
  • fermented food
  • beverages
  • cell factory

Published Papers (11 papers)

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Research

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19 pages, 2623 KiB  
Article
Development of a Vector Set for High or Inducible Gene Expression and Protein Secretion in the Yeast Genus Blastobotrys
by Anita Boisramé and Cécile Neuvéglise
J. Fungi 2022, 8(5), 418; https://0-doi-org.brum.beds.ac.uk/10.3390/jof8050418 - 19 Apr 2022
Cited by 1 | Viewed by 2091
Abstract
Converting lignocellulosic biomass into value-added products is one of the challenges in developing a sustainable economy. Attempts to engineer fermenting yeasts to recover plant waste are underway. Although intensive metabolic engineering has been conducted to obtain Saccharomyces cerevisiae strains capable of metabolising pentose [...] Read more.
Converting lignocellulosic biomass into value-added products is one of the challenges in developing a sustainable economy. Attempts to engineer fermenting yeasts to recover plant waste are underway. Although intensive metabolic engineering has been conducted to obtain Saccharomyces cerevisiae strains capable of metabolising pentose sugars mainly found in hemicellulose, enzymatic hydrolysis after pretreatment is still required. Blastobotrys raffinosifermentans, which naturally assimilates xylose and arabinose and displays numerous glycoside hydrolases, is a good candidate for direct and efficient conversion of renewable biomass. However, a greater diversity of tools for genetic engineering is needed. Here, we report the characterisation of four new promising promoters, a new dominant marker, and two vectors for the secretion of epitope tagged proteins along with a straightforward transformation protocol. The TDH3 promoter is a constitutive promoter stronger than TEF1, and whose activity is maintained at high temperature or in the presence of ethanol. The regulated promoters respond to high temperature for HSP26, gluconeogenic sources for PCK1 or presence of xylose oligomers for XYL1. Two expression/secretion vectors were designed based on pTEF1 and pTDH3, two endogenous signal peptides from an α-arabinanase and an α-glucuronidase, and two epitopes. A heterologous α-arabinoxylan hydrolase from Apiotrichum siamense was efficiently secreted using these two vectors. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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18 pages, 5973 KiB  
Article
Selection by UV Mutagenesis and Physiological Characterization of Mutant Strains of the Yeast Saprochaete suaveolens (Former Geotrichum fragrans) with Higher Capacity to Produce Flavor Compounds
by Melissa Tan, Yanis Caro, Alain Shum Cheong Sing, Héloïse Reiss, Jean-Marie Francois and Thomas Petit
J. Fungi 2021, 7(12), 1031; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7121031 - 30 Nov 2021
Cited by 4 | Viewed by 2753
Abstract
Yeast volatile organic compounds (VOCs), i.e. low molecular weight organic acids, alcohols and esters, are considered as potential and sustainable sources of natural aromas that can replace commonly used artificial flavors in food and other industrial sectors. Although research generally focuses on the [...] Read more.
Yeast volatile organic compounds (VOCs), i.e. low molecular weight organic acids, alcohols and esters, are considered as potential and sustainable sources of natural aromas that can replace commonly used artificial flavors in food and other industrial sectors. Although research generally focuses on the yeast Saccharomyces cerevisiae, other so-called unconventional yeasts (NCY) are beginning to attract the attention of researchers, particularly for their ability to produce alternative panels of VOCs. With this respect, a Saprochaete suaveolens strain isolated from dragon fruit in Reunion Island was shown to produce α-unsaturated esters from branched-chain amino acids (BCAAs) such as isobutyl, isoamyl or ethyl tiglate, which are rarely found in other yeasts strains. Given that β-oxidation allows the growth of S. suaveolens on BCAAs as sole carbon source, we developped a method based on UV mutagenesis to generate mutants that can no longer grow on BCAAs, while redirecting the carbon flow towards esterification of α-unsaturated esters. Among the 15,000 clones generated through UV irradiation, we identified nine clones unable to grow on BCAAs with one of them able to produce eight times more VOCs as compared to the wild-type strain. This higher production of α-unsaturated esters in this mutant strain coincided with an almost complete loss of enoyl-CoA hydratase activity of the β-oxidation pathways and with a twofold increase of acyl-CoA hydrolase with not significant changes in the enzymes of the Ehrlich pathway. Moreover, from our knowledge, it constituted the first example of VOCs enhancement in a microbial strain by UV mutagenesis. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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20 pages, 21671 KiB  
Article
Lebanon’s Native Oenological Saccharomyces cerevisiae Flora: Assessment of Different Aspects of Genetic Diversity and Evaluation of Winemaking Potential
by Marie-José Ayoub, Jean-Luc Legras, Pierre Abi-Nakhoul, Huu-Vang Nguyen, Rachad Saliba and Claude Gaillardin
J. Fungi 2021, 7(8), 678; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7080678 - 23 Aug 2021
Cited by 5 | Viewed by 2364
Abstract
A total of 296 isolates of Saccharomyces cerevisiae sampled from naturally fermenting grape musts from various locations in Lebanon were typed by interdelta fingerprinting. Of these, 88 isolates were compared with oenological strains originating from various countries, using microsatellite characterization at six polymorphic [...] Read more.
A total of 296 isolates of Saccharomyces cerevisiae sampled from naturally fermenting grape musts from various locations in Lebanon were typed by interdelta fingerprinting. Of these, 88 isolates were compared with oenological strains originating from various countries, using microsatellite characterization at six polymorphic loci. These approaches evidenced a large diversity of the natural oenological Lebanese flora over the territory as well as in individual spontaneous fermentations. Several cases of dominance and perenniality of isolates were observed in the same wineries, where fermentations appeared to involve lineages of sibling isolates. Our work thus evidenced a “winery effect” on strains’ relatedness. Similarly, related or identical strains were also detected in vicinal wineries, suggesting strain circulation within small geographical areas and a further “vicinity effect”. Moreover, and despite its diversity, the Lebanese flora seemed interrelated, on the basis of microsatellite loci analysis, in comparison to worldwide communities. We finally tested the ability of 21 indigenous strains to act as potential starters for winemaking. Seven of them passed our pre-selection scheme and two of them at least may be good candidates for use provided pilot-scale assays confirm their suitability. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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13 pages, 2043 KiB  
Article
Prediction of Genetic Groups within Brettanomyces bruxellensis through Cell Morphology Using a Deep Learning Tool
by Manon Lebleux, Emmanuel Denimal, Déborah De Oliveira, Ambroise Marin, Nicolas Desroche, Hervé Alexandre, Stéphanie Weidmann and Sandrine Rousseaux
J. Fungi 2021, 7(8), 581; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7080581 - 21 Jul 2021
Viewed by 2166
Abstract
Brettanomyces bruxellensis is described as a wine spoilage yeast with many mainly strain-dependent genetic characteristics, bestowing tolerance against environmental stresses and persistence during the winemaking process. Thus, it is essential to discriminate B. bruxellensis isolates at the strain level in order to predict [...] Read more.
Brettanomyces bruxellensis is described as a wine spoilage yeast with many mainly strain-dependent genetic characteristics, bestowing tolerance against environmental stresses and persistence during the winemaking process. Thus, it is essential to discriminate B. bruxellensis isolates at the strain level in order to predict their stress resistance capacities. Few predictive tools are available to reveal intraspecific diversity within B. bruxellensis species; also, they require expertise and can be expensive. In this study, a Random Amplified Polymorphic DNA (RAPD) adapted PCR method was used with three different primers to discriminate 74 different B. bruxellensis isolates. High correlation between the results of this method using the primer OPA-09 and those of a previous microsatellite analysis was obtained, allowing us to cluster the isolates among four genetic groups more quickly and cheaply than microsatellite analysis. To make analysis even faster, we further investigated the correlation suggested in a previous study between genetic groups and cell polymorphism using the analysis of optical microscopy images via deep learning. A Convolutional Neural Network (CNN) was trained to predict the genetic group of B. bruxellensis isolates with 96.6% accuracy. These methods make intraspecific discrimination among B. bruxellensis species faster, simpler and less costly. These results open up very promising new perspectives in oenology for the study of microbial ecosystems. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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23 pages, 4345 KiB  
Article
Marker Assisted Selection of Malic-Consuming Saccharomyces cerevisiae Strains for Winemaking. Efficiency and Limits of a QTL’s Driven Breeding Program
by Charlotte Vion, Emilien Peltier, Margaux Bernard, Maitena Muro and Philippe Marullo
J. Fungi 2021, 7(4), 304; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7040304 - 15 Apr 2021
Cited by 5 | Viewed by 2424
Abstract
Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. Breeding programs that take advantage of this characteristic are widely used for selecting starters for wine industry, especially in the recent years when winemakers need to adapt their production to climate [...] Read more.
Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. Breeding programs that take advantage of this characteristic are widely used for selecting starters for wine industry, especially in the recent years when winemakers need to adapt their production to climate change. The aim of this work was to evaluate a marker assisted selection (MAS) program to improve malic acid consumption capacity of Saccharomyces cerevisiae in grape juice. Optimal individuals of two unrelated F1-hybrids were crossed to get a new genetic background carrying many “malic consumer” loci. Then, eleven quantitative trait loci (QTLs) already identified were used for implementing the MAS breeding program. By this method, extreme individuals able to consume more than 70% of malic acid in grape juice were selected. These individuals were tested in different enological matrixes and compared to their original parental strains. They greatly reduced the malic acid content at the end of alcoholic fermentation, they appeared to be robust to the environment, and they accelerated the ongoing of malolactic fermentations by Oenococcus oeni. This study illustrates how MAS can be efficiently used for selecting industrial Saccharomyces cerevisiae strains with outlier properties for winemaking. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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17 pages, 3340 KiB  
Article
Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast
by Carolina Santiago, Teresa Rito, Daniel Vieira, Ticiana Fernandes, Célia Pais, Maria João Sousa, Pedro Soares and Ricardo Franco-Duarte
J. Fungi 2021, 7(4), 287; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7040287 - 10 Apr 2021
Cited by 10 | Viewed by 2371
Abstract
Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer [...] Read more.
Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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18 pages, 4834 KiB  
Article
Potential Probiotic Strains of Saccharomyces and Non-Saccharomyces: Functional and Biotechnological Characteristics
by Pilar Fernández-Pacheco, Cristina Pintado, Ana Briones Pérez and María Arévalo-Villena
J. Fungi 2021, 7(3), 177; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7030177 - 02 Mar 2021
Cited by 17 | Viewed by 2264
Abstract
Due to the evident demand for probiotic microorganisms, a growing number of scientific studies have involved the preliminary selection of new strains, but deeper studies for knowing specific functional and biotechnological properties are needed. In the present work, twenty yeasts (Saccharomyces and [...] Read more.
Due to the evident demand for probiotic microorganisms, a growing number of scientific studies have involved the preliminary selection of new strains, but deeper studies for knowing specific functional and biotechnological properties are needed. In the present work, twenty yeasts (Saccharomyces and non-Saccharomyces) with potential probiotic characteristics, selected in previous works, were evaluated. The following assays were realized: adhesion to Caco-2/TC7 cells, prebiotic metabolisms, assimilation of cholesterol, enzymatic and antioxidant activity, and antifungal resistance. In addition, the effect of ultrasonic treatment was evaluated for attenuating the cultures before their possible incorporation into a food or supplement. In all of the cases, the unique commercial probiotic yeast (S. boulardii CNM I-745) was used as positive control. Results show different capabilities depending on the property studied. In general, no Saccharomyces yeasts were better in the adhesion to Caco cells, prebiotic metabolism, and presented higher variability of enzymatic activities. The ones related to cholesterol assimilation and antioxidant capability did not show a marked trend, and with respect to the attenuation process, the Saccharomyces yeasts were more resistant. For selecting the potential probiotic yeasts with better balance among all characteristics, a principal component analysis (PCA) was carried out. The most promising yeasts for use as health-promoting probiotics are Hanseniaspora osmophila 1056 and 1094, Lachancea thermotolerans 1039, and S. cerevisiae 3 and 146. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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Review

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22 pages, 1822 KiB  
Review
Past, Present, and Future Perspectives on Whey as a Promising Feedstock for Bioethanol Production by Yeast
by Jing Zou and Xuedong Chang
J. Fungi 2022, 8(4), 395; https://0-doi-org.brum.beds.ac.uk/10.3390/jof8040395 - 12 Apr 2022
Cited by 16 | Viewed by 2899
Abstract
Concerns about fossil fuel depletion and the environmental effects of greenhouse gas emissions have led to widespread fermentation-based production of bioethanol from corn starch or sugarcane. However, competition for arable land with food production has led to the extensive investigation of lignocellulosic sources [...] Read more.
Concerns about fossil fuel depletion and the environmental effects of greenhouse gas emissions have led to widespread fermentation-based production of bioethanol from corn starch or sugarcane. However, competition for arable land with food production has led to the extensive investigation of lignocellulosic sources and waste products of the food industry as alternative sources of fermentable sugars. In particular, whey, a lactose-rich, inexpensive byproduct of dairy production, is available in stable, high quantities worldwide. This review summarizes strategies and specific factors essential for efficient lactose/whey fermentation to ethanol. In particular, we cover the most commonly used strains and approaches for developing high-performance strains that tolerate fermentation conditions. The relevant genes and regulatory systems controlling lactose utilization and sources of new genes are also discussed in detail. Moreover, this review covers the optimal conditions, various feedstocks that can be coupled with whey substrates, and enzyme supplements for increasing efficiency and yield. In addition to the historical advances in bioethanol production from whey, this review explores the future of yeast-based fermentation of lactose or whey products for beverage or fuel ethanol as a fertile research area for advanced, environmentally friendly uses of industrial waste products. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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67 pages, 2386 KiB  
Review
Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement
by Catherine Madzak
J. Fungi 2021, 7(7), 548; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7070548 - 10 Jul 2021
Cited by 63 | Viewed by 9158
Abstract
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of [...] Read more.
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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16 pages, 11934 KiB  
Review
Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12
by Nur Athirah Yusof, Noor Haza Fazlin Hashim and Izwan Bharudin
J. Fungi 2021, 7(7), 528; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7070528 - 30 Jun 2021
Cited by 28 | Viewed by 3964
Abstract
Psychrophilic organisms possess several adaptive strategies which allow them to sustain life at low temperatures between −20 to 20 °C. Studies on Antarctic psychrophiles are interesting due to the multiple stressors that exist on the permanently cold continent. These organisms produce, among other [...] Read more.
Psychrophilic organisms possess several adaptive strategies which allow them to sustain life at low temperatures between −20 to 20 °C. Studies on Antarctic psychrophiles are interesting due to the multiple stressors that exist on the permanently cold continent. These organisms produce, among other peculiarities, cold-active enzymes which not only have tremendous biotechnological potential but are valuable models for fundamental research into protein structure and function. Recent innovations in omics technologies such as genomics, transcriptomics, proteomics and metabolomics have contributed a remarkable perspective of the molecular basis underpinning the mechanisms of cold adaptation. This review critically discusses similar and different strategies of cold adaptation in the obligate psychrophilic yeast, Glaciozyma antarctica PI12 at the molecular (genome structure, proteins and enzymes, gene expression) and physiological (antifreeze proteins, membrane fluidity, stress-related proteins) levels. Our extensive studies on G. antarctica have revealed significant insights towards the innate capacity of- and the adaptation strategies employed by this psychrophilic yeast for life in the persistent cold. Furthermore, several cold-active enzymes and proteins with biotechnological potential are also discussed. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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19 pages, 2685 KiB  
Review
Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii
by Maria Sousa-Silva, Daniel Vieira, Pedro Soares, Margarida Casal and Isabel Soares-Silva
J. Fungi 2021, 7(1), 36; https://0-doi-org.brum.beds.ac.uk/10.3390/jof7010036 - 09 Jan 2021
Cited by 17 | Viewed by 6283
Abstract
Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic [...] Read more.
Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii. Full article
(This article belongs to the Special Issue Leveraging Yeast Biodiversity for Biotechnology)
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