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Rintarhat P, Cho YJ, Koh H, Park S, Lee EJ, Lim H, Noh J, Lee DW, Jung WH. Assessment of DNA extraction methods for human gut mycobiome analysis. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231129. [PMID: 38204788 PMCID: PMC10776226 DOI: 10.1098/rsos.231129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
The gut mycobiome plays an important role in the health and disease of the human gut, but its exact function is still under investigation. While there is a wealth of information available on the bacterial community of the human gut microbiome, research on the fungal community is still relatively limited. In particular, technical methodologies for mycobiome analysis, especially the DNA extraction method for human faecal samples, varied in different studies. In the current study, two commercial kits commonly used in DNA extraction, the QIAamp® Fast DNA Stool Mini Kit and DNeasy PowerSoil Pro Kit, and one manual method, the International Human Microbiome Standards Protocol Q, were compared. Furthermore, the effectiveness of two different bead-beating machines, the Mini-Beadbeater-16 and FastPrep-24TM 5G, was compared in parallel. A mock fungal community with a known composition of fungal strains was also generated and included to compare different DNA extraction methods. Our results suggested that the method using the DNeasy PowerSoil Pro Kit and Mini-Beadbeater-16 provides the best results to extract DNA from human faecal samples. Based on our data, we propose a standard operating procedure for DNA extraction from human faecal samples for mycobiome analysis.
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Affiliation(s)
- Piyapat Rintarhat
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, Kangwon National University, Chuncheon 24341, Korea
| | - Hong Koh
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sowon Park
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Joo Lee
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeji Lim
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jihye Noh
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
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Naumova ES, Lee CF, Naumov GI. Molecular Genetic Polymorphism of the Yeast Kluyveromyces dobzhanskii. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721040093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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3
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Pacheco A, Donzella L, Hernandez-Lopez MJ, Almeida MJ, Prieto JA, Randez-Gil F, Morrissey JP, Sousa MJ. Hexose transport in Torulaspora delbrueckii: identification of Igt1, a new dual-affinity transporter. FEMS Yeast Res 2021; 20:5715911. [PMID: 31981362 DOI: 10.1093/femsyr/foaa004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 01/24/2020] [Indexed: 01/23/2023] Open
Abstract
Torulaspora delbrueckii is a yeast species receiving increasing attention from the biotechnology industry, with particular relevance in the wine, beer and baking sectors. However, little is known about its sugar transporters and sugar transport capacity, frequently a rate-limiting step of sugar metabolism and efficient fermentation. Actually, only one glucose transporter, Lgt1, has been characterized so far. Here we report the identification and characterization of a second glucose transporter gene, IGT1, located in a cluster, upstream of LGT1 and downstream of two other putative hexose transporters. Functional characterization of IGT1 in a Saccharomyces cerevisiae hxt-null strain revealed that it encodes a transporter able to mediate uptake of glucose, fructose and mannose and established that its affinity, as measured by Km, could be modulated by glucose concentration in the medium. In fact, IGT1-transformed S. cerevisiae hxt-null cells, grown in 0.1% glucose displayed biphasic glucose uptake kinetics with an intermediate- (Km = 6.5 ± 2.0 mM) and a high-affinity (Km = 0.10 ± 0.01 mM) component, whereas cells grown in 2% glucose displayed monophasic kinetics with an intermediate-affinity (Km of 11.5 ± 1.5 mM). This work contributes to a better characterization of glucose transport in T. delbrueckii, with relevant implications for its exploitation in the food industry.
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Affiliation(s)
- Andreia Pacheco
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Lorena Donzella
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, T12YT20 Cork, Ireland
| | - Maria Jose Hernandez-Lopez
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - Maria Judite Almeida
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Jose Antonio Prieto
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, T12YT20 Cork, Ireland
| | - Maria João Sousa
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast. J Fungi (Basel) 2021; 7:jof7040287. [PMID: 33920164 PMCID: PMC8070057 DOI: 10.3390/jof7040287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/15/2022] Open
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 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.
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5
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Catrileo D, Acuña-Fontecilla A, Godoy L. Adaptive Laboratory Evolution of Native Torulaspora delbrueckii YCPUC10 With Enhanced Ethanol Resistance and Evaluation in Co-inoculated Fermentation. Front Microbiol 2021; 11:595023. [PMID: 33408704 PMCID: PMC7779481 DOI: 10.3389/fmicb.2020.595023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
Torulaspora delbrueckii is a yeast species typically present in the early stages of the fermentation process. T. delbrueckii positively modifies the aromatic properties of wines. However, its contribution to the final quality of the wine is restricted by its low tolerance to ethanol. T. delbrueckii is capable of fermenting and tolerating an ethanol concentration ranging from 7.4% (v/v) to slightly higher than 9% (v/v). For this reason, it cannot complete fermentation, when alcohol reach levels higher than 12% (v/v), limiting their use in the industry. The objective of this work was to obtain new variants of T. delbrueckii with improved resistance to ethanol through adaptive laboratory evolution. Variants capable of tolerating ethanol levels of 11.5% (v/v) were obtained. These presented improved kinetic parameters, and additionally showed an increase in resistance to SO2 in ethanol compared to the original strain. Co-inoculated fermentations were performed with the original strain (FTd/Sc) and with the evolved strain (FTdF/Sc), in addition to a control fermentation using only Saccharomyces cerevisiae EC1118 (FSc). The results obtained show that FTdF/Sc present higher levels of 2-Ethylhexanol, compared to FTd/Sc and FSc. Furthermore, FTdF/Sc presents higher levels of total alcohols, total aldehydes, total phenolic derivatives, and total sulfur compounds with significant differences with FSc. These results provide a T. delbrueckii YCPUC10-F yeast with higher resistance to ethanol, which can be present throughout the fermentation process and be used in co-inoculated fermentations. This would positively impact the performance of T. delbrueckii by allowing it to be present not only in the early stages of fermentation but to remain until the end of fermentation.
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Affiliation(s)
- Daniela Catrileo
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea Acuña-Fontecilla
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Liliana Godoy
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
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6
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Bensasson D, Dicks J, Ludwig JM, Bond CJ, Elliston A, Roberts IN, James SA. Diverse Lineages of Candida albicans Live on Old Oaks. Genetics 2019; 211:277-288. [PMID: 30463870 PMCID: PMC6325710 DOI: 10.1534/genetics.118.301482] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/05/2018] [Indexed: 12/26/2022] Open
Abstract
The human pathogen Candida albicans is considered an obligate commensal of animals, yet it is occasionally isolated from trees, shrubs, and grass. We generated genome sequence data for three strains of C. albicans that we isolated from oak trees in an ancient wood pasture, and compared these to the genomes of over 200 clinical strains. C. albicans strains from oak are similar to clinical C. albicans in that they are predominantly diploid and can become homozygous at the mating locus through whole-chromosome loss of heterozygosity. Oak strains differed from clinical strains in showing slightly higher levels of heterozygosity genome-wide. Using phylogenomic analyses and in silico chromosome painting, we show that each oak strain is more closely related to strains from humans and other animals than to strains from other oaks. The high genetic diversity of C. albicans from old oaks shows that they can live in this environment for extended periods of time.
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Affiliation(s)
- Douda Bensasson
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Jo Dicks
- National Collection of Yeast Cultures, Quadram Institute Bioscience, Norwich NR4 7UA, UK
| | - John M Ludwig
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Christopher J Bond
- National Collection of Yeast Cultures, Quadram Institute Bioscience, Norwich NR4 7UA, UK
| | - Adam Elliston
- National Collection of Yeast Cultures, Quadram Institute Bioscience, Norwich NR4 7UA, UK
| | - Ian N Roberts
- National Collection of Yeast Cultures, Quadram Institute Bioscience, Norwich NR4 7UA, UK
| | - Stephen A James
- National Collection of Yeast Cultures, Quadram Institute Bioscience, Norwich NR4 7UA, UK
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Abstract
Torulaspora delbrueckii is probably the non-Saccharomyces yeast that is currently most used for winemaking. Multiple advantages have been claimed for it relative to conventional S. cerevisiae strains. However, many of these claimed advantages are based on results in different research studies that are contradictory or non-reproducible. The easiest way to explain these discrepancies is to attribute them to the possible differences in the behaviour of the different strains of this yeast that have been used in different investigations. There is much less knowledge of the physiology, genetics, and biotechnological properties of this yeast than of the conventional yeast S. cerevisiae. Therefore, it is possible that the different results that have been found in the literature are due to the variable or unpredictable behaviour of T. delbrueckii, which may depend on the environmental conditions during wine fermentation. The present review focusses on the analysis of this variable behaviour of T. delbrueckii in the elaboration of different wine types, with special emphasis on the latest proposals for industrial uses of this yeast.
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Aljohani R, Samarasinghe H, Ashu T, Xu J. Diversity and relationships among strains of culturable yeasts in agricultural soils in Cameroon. Sci Rep 2018; 8:15687. [PMID: 30356081 PMCID: PMC6200750 DOI: 10.1038/s41598-018-34122-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 10/06/2018] [Indexed: 12/27/2022] Open
Abstract
Yeasts are unicellular fungi; they are found in a diverse range of natural habitats, including soil, aquatic environments, the surface of plants, and the skin and mucosal surfaces of animal hosts. A variety of yeasts have been found in the soil environment. However, most studies of soil yeasts have come from developed countries, and there is a dearth of research on soil yeasts in Africa. In this study, we analyzed 493 soil samples from nine geographical locations in Cameroon for yeasts, using a culture - based method. A total of 110 yeast isolates were obtained. Based on their sequences at the fungal barcode locus, the Internal Transcribed Spacer (ITS) regions of the nuclear ribosomal RNA gene cluster, the 110 yeast isolates were putatively identified as belonging to 16 yeast species, including 15 Ascomycetes and one Basidiomycete. Differences in yeast species distribution were observed among the analyzed geographic regions. PCR fingerprinting analyses identified a large number of genotypes among strains within each of the obtained yeast species. Significantly, there was little evidence of geographic clustering among yeast strains from any of the yeast species. Our results suggest that Cameroon contains significant yeast diversity and that gene flow is common among local and regional soil yeast populations.
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Affiliation(s)
- Renad Aljohani
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, Ontario, L8S 4K1, Canada
| | - Himeshi Samarasinghe
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, Ontario, L8S 4K1, Canada
| | - Tabi Ashu
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, Ontario, L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, 1280 Main St West, Hamilton, Ontario, L8S 4K1, Canada.
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9
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Naumova ES, Sadykova AZ, Martynenko NN, Naumov GI. Hybrid Selection of Saccharomyces cerevisiae Yeasts for Thermotolerance and Fermentation Activity. Microbiology (Reading) 2018. [DOI: 10.1134/s002626171802008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Liti G, Warringer J, Blomberg A. Isolation and Laboratory Domestication of Natural Yeast Strains. Cold Spring Harb Protoc 2017; 2017:pdb.prot089052. [PMID: 28765292 DOI: 10.1101/pdb.prot089052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The process from yeast isolation to their use in laboratory experiments is lengthy. Historically, Saccharomyces strains were easily obtained by sampling alcoholic fermentation processes or other substrates associated with human activity in which Saccharomyces was heavily enriched. In contrast, wild Saccharomyces yeasts are found in complex microbial communities and small population sizes, making isolation challenging. We have overcome this problem by enriching yeast on media favoring the growth of Saccharomyces over other microorganisms. The isolation process is usually followed by molecular characterization that allows the strain identification. Finally, yeast isolated from domestic or wild environments need to be genetically manipulated before they can be used in laboratory experiments.
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Affiliation(s)
- Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, 06107 Nice, France;
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), 1432 Ås, Norway
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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Naseeb S, James SA, Alsammar H, Michaels CJ, Gini B, Nueno-Palop C, Bond CJ, McGhie H, Roberts IN, Delneri D. Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur. Int J Syst Evol Microbiol 2017. [PMID: 28639933 PMCID: PMC5817255 DOI: 10.1099/ijsem.0.002013] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Two strains, D5088T and D5095, representing a novel yeast species belonging to the genus Saccharomyces were isolated from oak tree bark and surrounding soil located at an altitude of 1000 m above sea level in Saint Auban, France. Sequence analyses of the internal transcribed spacer (ITS) region and 26S rRNA D1/D2 domains indicated that the two strains were most closely related to Saccharomyces mikatae and Saccharomyces paradoxus. Genetic hybridization analyses showed that both strains are reproductively isolated from all other Saccharomyces species and, therefore, represent a distinct biological species. The species name Saccharomyces jurei sp. nov. is proposed to accommodate these two strains, with D5088T (=CBS 14759T=NCYC 3947T) designated as the type strain.
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Affiliation(s)
- Samina Naseeb
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | | | - Haya Alsammar
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | - Christopher J. Michaels
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | - Beatrice Gini
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | | | | | - Henry McGhie
- The Manchester Museum, The University of Manchester, Manchester M13 9PL, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
- *Correspondence: Daniela Delneri,
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12
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Naumova ES, Lee CF, Kondratieva VI, Sadykova AZ, Naumov GI. Molecular genetic polymorphism of soil yeasts of the genus Williopsis from Taiwan Island. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417040111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mukherjee V, Radecka D, Aerts G, Verstrepen KJ, Lievens B, Thevelein JM. Phenotypic landscape of non-conventional yeast species for different stress tolerance traits desirable in bioethanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:216. [PMID: 28924451 PMCID: PMC5597992 DOI: 10.1186/s13068-017-0899-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/04/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Non-conventional yeasts present a huge, yet barely exploited, resource of yeast biodiversity for industrial applications. This presents a great opportunity to explore alternative ethanol-fermenting yeasts that are more adapted to some of the stress factors present in the harsh environmental conditions in second-generation (2G) bioethanol fermentation. Extremely tolerant yeast species are interesting candidates to investigate the underlying tolerance mechanisms and to identify genes that when transferred to existing industrial strains could help to design more stress-tolerant cell factories. For this purpose, we performed a high-throughput phenotypic evaluation of a large collection of non-conventional yeast species to identify the tolerance limits of the different yeast species for desirable stress tolerance traits in 2G bioethanol production. Next, 12 multi-tolerant strains were selected and used in fermentations under different stressful conditions. Five strains out of which, showing desirable fermentation characteristics, were then evaluated in small-scale, semi-anaerobic fermentations with lignocellulose hydrolysates. RESULTS Our results revealed the phenotypic landscape of many non-conventional yeast species which have not been previously characterized for tolerance to stress conditions relevant for bioethanol production. This has identified for each stress condition evaluated several extremely tolerant non-Saccharomyces yeasts. It also revealed multi-tolerance in several yeast species, which makes those species good candidates to investigate the molecular basis of a robust general stress tolerance. The results showed that some non-conventional yeast species have similar or even better fermentation efficiency compared to S. cerevisiae in the presence of certain stressful conditions. CONCLUSION Prior to this study, our knowledge on extreme stress-tolerant phenotypes in non-conventional yeasts was limited to only few species. Our work has now revealed in a systematic way the potential of non-Saccharomyces species to emerge either as alternative host species or as a source of valuable genetic information for construction of more robust industrial S. serevisiae bioethanol production yeasts. Striking examples include yeast species like Pichia kudriavzevii and Wickerhamomyces anomalus that show very high tolerance to diverse stress factors. This large-scale phenotypic analysis has yielded a detailed database useful as a resource for future studies to understand and benefit from the molecular mechanisms underlying the extreme phenotypes of non-conventional yeast species.
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Affiliation(s)
- Vaskar Mukherjee
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, VIB Center of Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Louvain, Belgium
- Laboratory for Enzyme, Fermentation and Brewing Technology (EFBT), Department of Microbial and Molecular Systems, KU Leuven, Technology Campus Ghent, Gebroeders De Smetstraat 1, B-9000 Ghent, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium
- Present Address: Lundberg Laboratory, Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390 Göteborg, Sweden
| | - Dorota Radecka
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, VIB Center of Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Louvain, Belgium
| | - Guido Aerts
- Laboratory for Enzyme, Fermentation and Brewing Technology (EFBT), Department of Microbial and Molecular Systems, KU Leuven, Technology Campus Ghent, Gebroeders De Smetstraat 1, B-9000 Ghent, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Systems Biology, VIB Center for Microbiology, KU Leuven, Gaston Geenslaan 1, B-3001 Louvain, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, VIB Center of Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Louvain, Belgium
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14
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James SA, Bond CJ, Stanley R, Ravella SR, Péter G, Dlauchy D, Roberts IN. Apiotrichum terrigenum sp. nov., a soil-associated yeast found in both the UK and mainland Europe. Int J Syst Evol Microbiol 2016; 66:5046-5050. [PMID: 27580597 PMCID: PMC5244499 DOI: 10.1099/ijsem.0.001467] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five arthroconidium-producing yeast strains representing a novel Trichosporon-like species were independently isolated from the UK, Hungary and Norway. Two strains (Bio4T and Bio21) were isolated from biogas reactors used for processing grass silage, with a third strain (S8) was isolated from soil collected at the same UK site. Two additional strains were isolated in mainland Europe, one from soil in Norway (NCAIM Y.02175) and the other from sewage in Hungary (NCAIM Y.02176). Sequence analyses of the D1/D2 domains of the LSU rRNA gene and internal transcribed spacer (ITS) region indicated that the novel species belongs to the recently reinstated genus Apiotrichum and is most closely related to Apiotrichum scarabaeorum, a beetle-associated species first found in South Africa. Despite having similar physiological characteristics, the two species can be readily distinguished from one another by ITS sequencing. The species name Apiotrichum terrigenum sp. nov. is proposed to accommodate these strains, with Bio4T (=CBS 11373T=NCYC 3540T) designated as the type strain. The Mycobank deposit number is MB817431.
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Affiliation(s)
- Stephen A James
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Christopher J Bond
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Rachael Stanley
- Imaging and Microscopy Group (IMG), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Sreenivas R Ravella
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, UK
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Budapest, Hungary
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Budapest, Hungary
| | - Ian N Roberts
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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15
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Chand Dakal T, Giudici P, Solieri L. Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex. PLoS One 2016; 11:e0160744. [PMID: 27501051 PMCID: PMC4976873 DOI: 10.1371/journal.pone.0160744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding.
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Affiliation(s)
- Tikam Chand Dakal
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
- * E-mail:
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Wu ZW, Wang QM, Liu XZ, Bai FY. Intragenomic polymorphism and intergenomic recombination in the ribosomal RNA genes of strains belonging to a yeast species Pichia membranifaciens. Mycology 2016; 7:102-111. [PMID: 30123622 PMCID: PMC6059064 DOI: 10.1080/21501203.2016.1204369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/12/2016] [Indexed: 11/30/2022] Open
Abstract
A concerted evolution model has been proposed to explain the observed lack of sequence variation among the multiple ribosomal RNA (rRNA) gene copies in many different eukaryotic species. Recent studies on the level of intragenomic variations in the rRNA gene repeats of fungi resulted in controversial conclusions. In this study, we clearly showed that significant polymorphisms of the internal transcribed spacers (ITS1 and ITS2) of ribosomal DNA (rDNA) exist within the genome of a strain of the yeast species Pichia membranifaciens. More interestingly, we showed that the intragenomic ITS sequence polymorphisms were formed by intergenomic rDNA recombination among different P. membranifaciens strains with significantly different ITS sequences. Intergenomic rDNA recombination was also responsible for the diversification of rDNA sequences in different strains of the species. After the events bring together different rDNA types in individual genomes of the P. membranifaciens strains compared, rDNA sequence heterogeneity has remained in the genome of one but eliminated by homogenisation in the genomes of other strains. Our findings show new clue for further investigation on the mechanism of concerted evolution of rRNA genes in eukaryotes.
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Affiliation(s)
- Zuo-Wei Wu
- State key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi-Ming Wang
- State key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Zhan Liu
- State key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng-Yan Bai
- State key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Yee TL, Tajuddin R, Mohamed Nor NMI, Mohd MH, Zakaria L. Filamentous ascomycete and basidiomycete fungi from beach sand. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2016. [DOI: 10.1007/s12210-016-0535-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Kopecká J, Němec M, Matoulková D. Comparison of DNA-based techniques for differentiation of production strains of ale and lager brewing yeast. J Appl Microbiol 2016; 120:1561-73. [PMID: 26929399 DOI: 10.1111/jam.13116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 01/05/2016] [Accepted: 02/18/2016] [Indexed: 11/28/2022]
Abstract
AIMS Brewing yeasts are classified into two species-Saccharomyces pastorianus and Saccharomyces cerevisiae. Most of the brewing yeast strains are natural interspecies hybrids typically polyploids and their identification is thus often difficult giving heterogenous results according to the method used. We performed genetic characterization of a set of the brewing yeast strains coming from several yeast culture collections by combination of various DNA-based techniques. The aim of this study was to select a method for species-specific identification of yeast and discrimination of yeast strains according to their technological classification. METHODS AND RESULTS A group of 40 yeast strains were characterized using PCR-RFLP analysis of ITS-5·8S, NTS, HIS4 and COX2 genes, multiplex PCR, RAPD-PCR of genomic DNA, mtDNA-RFLP and electrophoretic karyotyping. Reliable differentiation of yeast to the species level was achieved by PCR-RFLP of HIS4 gene. Numerical analysis of the obtained RAPD-fingerprints and karyotype revealed species-specific clustering corresponding with the technological classification of the strains. Taxonomic position and partial hybrid nature of strains were verified by multiplex PCR. Differentiation among species using the PCR-RFLP of ITS-5·8S and NTS region was shown to be unreliable. Karyotyping and RFLP of mitochondrial DNA evinced small inaccuracies in strain categorization. CONCLUSIONS PCR-RFLP of HIS4 gene and RAPD-PCR of genomic DNA are reliable and suitable methods for fast identification of yeast strains. RAPD-PCR with primer 21 is a fast and reliable method applicable for differentiation of brewing yeasts with only 35% similarity of fingerprint profile between the two main technological groups (ale and lager) of brewing strains. SIGNIFICANCE AND IMPACT OF THE STUDY It was proved that PCR-RFLP method of HIS4 gene enables precise discrimination among three technologically important Saccharomyces species. Differentiation of brewing yeast to the strain level can be achieved using the RAPD-PCR technique.
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Affiliation(s)
- J Kopecká
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - M Němec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - D Matoulková
- Department of Microbiology, Research Institute of Brewing and Malting, Praha, Czech Republic
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Chang CF, Lee CF, Lin KY, Liu SM. Diversity of yeasts associated with the sea surface microlayer and underlying water along the northern coast of Taiwan. Res Microbiol 2016; 167:35-45. [DOI: 10.1016/j.resmic.2015.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/07/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
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James SA, Carvajal Barriga EJ, Portero Barahona P, Nueno-Palop C, Cross K, Bond CJ, Roberts IN. Kazachstania yasuniensis sp. nov., an ascomycetous yeast species found in mainland Ecuador and on the Galápagos. Int J Syst Evol Microbiol 2015; 65:1304-1309. [DOI: 10.1099/ijs.0.000102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven strains representing a novel yeast species belonging to the genus Kazachstania were found at several collection sites on both mainland Ecuador (Yasuní National Park) and the Galápagos (Santa Cruz Island). Two strains (CLQCA 20-132T and CLQCA 24SC-045) were isolated from rotten wood samples, two further strains (CLQCA 20-280 and CLQCA 20-348) were isolated from soil samples, and three strains (CLQCA 20-198, CLQCA 20-374 and CLQCA 20-431) were isolated from decaying fruits. Sequence analyses of the D1/D2 domains of the LSU rRNA gene and ribosomal internal transcribed spacer (ITS) region indicated that the novel species is most closely related to Kazachstania servazzii and Kazachstania unispora. Although the strains could not be distinguished from one another based upon their differing geographical origins, they could be differentiated according to their isolation source (fruit, soil or wood) by ITS sequencing. The species name Kazachstania yasuniensis sp. nov. is proposed to accommodate these strains, with CLQCA 20-132T ( = CBS 13946T = NCYC 4008T) designated the type strain.
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Affiliation(s)
- Stephen A. James
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Enrique Javier Carvajal Barriga
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Patricia Portero Barahona
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Carmen Nueno-Palop
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Kathryn Cross
- Imaging and Microscopy Group (IMG), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Christopher J. Bond
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Ian N. Roberts
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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21
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Candida inconspicua and Candida norvegensis: new insights into identification in relation to sexual reproduction and genome organization. J Clin Microbiol 2015; 53:1655-61. [PMID: 25762773 DOI: 10.1128/jcm.02913-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/05/2015] [Indexed: 01/22/2023] Open
Abstract
Candida inconspicua and Candida (Pichia) norvegensis are two emerging pathogenic species that exhibit reduced susceptibility to azole derivatives. Conventional (biochemical) approaches do not readily differentiate between the two species. The first aim of this work was to analyze the performance of biochemical, proteomic (matrix-assisted laser desorption ionization-time of flight [MALDI-TOF]), and molecular approaches in the precise identification of these species. These results then led us to sequence 3 genomic loci, i.e., the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), the D1/D2 domain of the 28S rDNA, and the elongation factor 1α (EF-1α) gene, either directly or following cloning, of 13 clinical isolates and 9 reference strains belonging to the 5 species included in the Pichia cactophila clade, namely, Pichia cactophila, Pichia insulana, C. inconspicua, C. norvegensis, and P. pseudocactophila. Finally, isolates of C. inconspicua were challenged for sexual reproduction on the appropriate medium. Our results show that EF-1α sequencing and proteic profiling by MALDI-TOF are the two most efficient approaches to distinguish between C. norvegensis and C. inconspicua. As a characteristic of the P. cactophila clade, we found multiple alleles of the rDNA regions in certain strains belonging to the tested species, making ITS or D1/D2 sequencing not appropriate for identification. Whatever the method of identification, including MALDI-TOF and EF-1α sequencing, none could differentiate C. inconspicua from P. cactophila. The results of phylogenetic analysis and the generation of asci from pure cultures of all C. inconspicua strains both support the identification of P. cactophila as the teleomorph of C. inconspicua.
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22
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Parker N, James S, Dicks J, Bond C, Nueno-Palop C, White C, Roberts IN. Investigating flavour characteristics of British ale yeasts: techniques, resources and opportunities for innovation. Yeast 2014; 32:281-7. [PMID: 25361168 PMCID: PMC4383656 DOI: 10.1002/yea.3052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/24/2014] [Accepted: 10/26/2014] [Indexed: 11/28/2022] Open
Abstract
Five British ale yeast strains were subjected to flavour profiling under brewery fermentation conditions in which all other brewing parameters were kept constant. Significant variation was observed in the timing and quantity of flavour-related chemicals produced. Genetic tests showed no evidence of hybrid origins in any of the strains, including one strain previously reported as a possible hybrid of Saccharomyces cerevisiae and S. bayanus. Variation maintained in historical S. cerevisiae ale yeast collections is highlighted as a potential source of novelty in innovative strain improvement for bioflavour production. Copyright © 2014 John Wiley & Sons, Ltd.
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Affiliation(s)
- Neva Parker
- White Labs, 9495 Candida Street, San Diego, CA, 92126, USA
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23
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24
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Hesham AEL, Wambui V, Ogola J.O. H, Maina JM. Phylogenetic analysis of isolated biofuel yeasts based on 5.8S-ITS rDNA and D1/D2 26S rDNA sequences. J Genet Eng Biotechnol 2014. [DOI: 10.1016/j.jgeb.2014.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Genotyping of a Miso and Soy Sauce Fermentation Yeast,Zygosaccharomyces rouxii, Based on Sequence Analysis of the Partial 26S Ribosomal RNA Gene and Two Internal Transcribed Spacers. Biosci Biotechnol Biochem 2014; 72:2452-5. [DOI: 10.1271/bbb.80211] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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James SA, Barriga EJC, Barahona PP, Harrington TC, Lee CF, Bond CJ, Roberts IN. Wickerhamomyces arborarius f.a., sp. nov., an ascomycetous yeast species found in arboreal habitats on three different continents. Int J Syst Evol Microbiol 2014; 64:1057-1061. [PMID: 24453230 DOI: 10.1099/ijs.0.059162-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains representing a novel yeast species belonging to the genus Wickerhamomyces were independently isolated from Ecuador, Taiwan and the USA. One strain (CLQCA 10-161(T)) was isolated from the white flower of an unidentified plant species collected in the Maquipucuna cloud forest reserve, near Quito, in Ecuador. A second strain (GY7L12) was isolated from the leaf of a Chinese sumac or nutgall tree (Rhus chinensis 'roxburghiana') collected in the Taoyuan mountain area, Kachsiung, in Taiwan. Three additional strains (A543, A546 and A563) were isolated from two species of wood-boring beetle (Xyleborus glabratus and Xyleborinus saxeseni) collected near Clyo, Georgia, USA. Analysis of the D1/D2 domains of the LSU rRNA gene indicated that the novel species belongs to the genus Wickerhamomyces, and is most closely related to Wickerhamomyces sydowiorum, an insect-associated species predominantly found in South Africa. The North American and Taiwanese strains have identical internal transcribed spacer (ITS) sequences and can be distinguished from the Ecuadorian strain based on a single nucleotide substitution in the ITS1 region. The species name of Wickerhamomyces arborarius f.a., sp. nov. is proposed to accommodate these strains, with CLQCA 10-161(T) ( = CBS 12941(T) = NCYC 3743(T)) designated the type strain.
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Affiliation(s)
- Stephen A James
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
| | - Enrique Javier Carvajal Barriga
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Patricia Portero Barahona
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Thomas C Harrington
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ching-Fu Lee
- Department of Applied Science, National Hsinchu University of Education, Hsinchu, Taiwan, ROC
| | - Christopher J Bond
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
| | - Ian N Roberts
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
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Weiss S, Samson F, Navarro D, Casaregola S. YeastIP: a database for identification and phylogeny ofSaccharomycotinayeasts. FEMS Yeast Res 2013; 13:117-25. [DOI: 10.1111/1567-1364.12017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/18/2012] [Accepted: 10/23/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
| | - Franck Samson
- INRA; UR 1077 Mathématique Informatique et Génome (MIG); Domaine de Vilvert; Jouy-en-Josas; France
| | - David Navarro
- INRA; UMR-1163 Biotechnologie des Champignons Filamenteux; ESIL; Marseille; France
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28
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Suh SO, Gujjari P, Beres C, Beck B, Zhou J. Proposal of Zygosaccharomyces parabailii sp. nov. and Zygosaccharomyces pseudobailii sp. nov., novel species closely related to Zygosaccharomyces bailii. Int J Syst Evol Microbiol 2013; 63:1922-1929. [PMID: 23524351 DOI: 10.1099/ijs.0.048058-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twenty-three yeast strains traditionally identified as Zygosaccharomyces bailii were studied in order to clarify their taxonomy and phylogenetic relationships. The molecular phylogeny from rRNA gene sequences showed that these yeasts were well divided into three major groups, and two of the groups could be clearly distinguished from the type strain of Z. bailii at the species level. Therefore, we propose Zygosaccharomyces parabailii sp. nov. (type strain ATCC 56075(T) = NBRC 1047(T) = NCYC 128(T) = CBS 12809(T)) and Zygosaccharomyces pseudobailii sp. nov. (type strain ATCC 56074(T) = NBRC 0488(T) = CBS 2856(T)) to accommodate the yeasts belonging to the two groups. By conventional physiological tests, Z. bailii and the two novel species are not clearly distinguished from one another, as variations exist more frequently between individual strains and are not species-specific. However, the conclusions from rRNA gene sequence analyses are well supported by genome fingerprinting patterns as well as other protein-coding gene sequence comparisons.
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Affiliation(s)
- Sung-Oui Suh
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
| | - Pushpa Gujjari
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
| | - Carolyn Beres
- bioMérieux, Inc., 595 Anglum Road, Hazelwood, MO 63042, USA
| | - Brian Beck
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
| | - Jianlong Zhou
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
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30
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James SA, Carvajal Barriga EJ, Barahona PP, Cross K, Bond CJ, Roberts IN. Candida ecuadorensis sp. nov., an ascomycetous yeast species found in two separate regions of Ecuador. Int J Syst Evol Microbiol 2013; 63:393-397. [DOI: 10.1099/ijs.0.047555-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the course of an on-going study aimed at cataloguing the natural yeast biodiversity found in Ecuador, two strains (CLQCA 13-025 and CLQCA 20-004T) were isolated from samples of cow manure and rotten wood collected in two separate provinces of the country (Orellana and Bolívar). These strains were found to represent a novel yeast species based on the sequences of their D1/D2 domain of the large-subunit (LSU) rRNA gene and their physiological characteristics. Phylogenetic analysis based on LSU D1/D2 sequences revealed this novel species to belong to the Metschnikowia clade and to be most closely related to Candida suratensis, a species recently discovered in a mangrove forest in Thailand. The species name of Candida ecuadorensis sp. nov. is proposed to accommodate these strains, with strain CLQCA 20-004T ( = CBS 12653T = NCYC 3782T) designated as the type strain.
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Affiliation(s)
- Stephen A. James
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Enrique Javier Carvajal Barriga
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Patricia Portero Barahona
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Kathryn Cross
- Imaging and Microscopy Group (IMG), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Christopher J. Bond
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Ian N. Roberts
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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31
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Two new anamorphic yeasts species, Cyberlindnera samutprakarnensis sp. nov. and Candida thasaenensis sp. nov., isolated from industrial wastes in Thailand. Antonie van Leeuwenhoek 2012; 103:229-38. [DOI: 10.1007/s10482-012-9804-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 08/25/2012] [Indexed: 11/26/2022]
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32
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Mokhtari M, Etebarian HR, Razavi M, Heydari A, Mirhendi H. Identification of Yeasts Isolated from Varieties of Apples and Citrus Using PCR-Fragment Size Polymorphism and Sequencing of ITS1–5.8S-ITS2 region. FOOD BIOTECHNOL 2012. [DOI: 10.1080/08905436.2012.698771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Naumova ES, Naumov GI, Nikitina TN, Sadykova AZ, Kondratieva VI. Molecular genetic and physiological differentiation of Kluyveromyces lactis and Kluyveromyces marxianus: Analysis of strains from the all-Russian collection of microorganisms (VKM). Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712020087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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34
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Tofalo R, Schirone M, Perpetuini G, Suzzi G, Corsetti A. Development and application of a real-time PCR-based assay to enumerate total yeasts and Pichia anomala, Pichia guillermondii and Pichia kluyveri in fermented table olives. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.07.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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35
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James SA, Cadet GM, Carvajal Barriga EJ, Barahona PP, Cross K, Bond CJ, Roberts IN. Saturnispora quitensis sp. nov., a yeast species isolated from the Maquipucuna cloud forest reserve in Ecuador. Int J Syst Evol Microbiol 2011; 61:3072-3076. [DOI: 10.1099/ijs.0.030759-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A single strain, CLQCA-10-114T, representing a novel yeast species belonging to the genus Saturnispora was isolated from the fruit of an unidentified species of bramble (Rubus sp.), collected from the Maquipucuna cloud forest reserve, near Quito, in Ecuador. Sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and ribosomal internal transcribed spacer region indicated that the novel species is most closely related to the recently described species Saturnispora gosingensis, isolated from the fruiting body of a mushroom collected in Taiwan, and Saturnispora hagleri, a Drosophila-associated yeast found in Brazil. The name Saturnispora quitensis sp. nov. is proposed to accommodate this strain; the type strain is CLQCA-10-114T ( = CBS 12184T = NCYC 3744T).
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Affiliation(s)
- Stephen A. James
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
| | - Geneviève M. Cadet
- Institut Universitaire de Technologie (IUT) de Saint-Pierre, Département Génie Biologique, Saint-Pierre, Ile de la Réunion
| | - Enrique Javier Carvajal Barriga
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Patricia Portero Barahona
- Colección de Levaduras Quito Católica (CLQCA), Centro Neotropical para Investigación de la Biomasa, Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Kathryn Cross
- Imaging and Microscopy Group (IMG), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
| | - Christopher J. Bond
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
| | - Ian N. Roberts
- National Collection of Yeast Cultures (NCYC), Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
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36
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Feng J, Zhan XB, Wang D, Zhang LM, Lin CC. Identification and analysis of the metabolic functions of a high-salt-tolerant halophilic aromatic yeast Candida etchellsii for soy sauce production. World J Microbiol Biotechnol 2011; 28:1451-8. [DOI: 10.1007/s11274-011-0945-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/03/2011] [Indexed: 10/15/2022]
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37
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Candida northwykensis sp. nov., A Novel Yeast Isolated from the Gut of the Click Beetle Melanotus villosus. Curr Microbiol 2011; 63:115-20. [DOI: 10.1007/s00284-011-9952-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 04/18/2011] [Indexed: 11/26/2022]
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38
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Mokhtari M, Etebarian H, Mirhendi S, Razavi M. Identification and phylogeny of some species of the genera Sporidiobolus and Rhodotorula using analysis of the 5.8s rDNA gene and two ribosomal internal transcribed spacers. ARCH BIOL SCI 2011. [DOI: 10.2298/abs1101079m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Due to the problems encountered in routine morphological and physiological
procedures that are used in yeast identification, DNA-based methods have
recently been developed. In the present study, l66 yeast strains were
isolated from several apple and citrus cultivars. After analysis by basic
morphological methods, the ITS1 and ITS2 regions of the isolates were
amplified separately, and the isolates were grouped based on fragment size
polymorphism (FSP) of the amplicons. By comparing the electrophoretic
patterns of the PCR products with Rhodotorula mucilaginosa, species were
identified as Rhodotorula. For precise and final identification, the ITS-PCR
products were subjected to sequencing followed by Blast analysis. As a
result, eight isolates were identified as belonging to the Rhodotorula genus,
of which five were identified as R. mucilaginosa and three as R. glutinis,
and one as a Sporidiobolus. We conclude that the method PCR-FSP, in
combination with other approaches, is useful for the identification of yeast
species.
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Affiliation(s)
- M. Mokhtari
- Plant Protection Dept., Abourayhan Campus, University of Tehran, Teheran, Iran
| | - H.R. Etebarian
- Plant Protection Dept., Abourayhan Campus, University of Tehran, Teheran, Iran
| | - S.H. Mirhendi
- Department of Medical Parasitology and Mycology, Faculty of Public Health, Tehran University of Medical Sciences, Teheran, Iran
| | - M. Razavi
- Iranian Research Institute of Plant Protection, Teheran, Iran
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39
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Naumova ES, Serpova EV, Naumov GI. Genome variability of the yeast Yarrowia lipolytica. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710020153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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40
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Carvalho CM, Rocha A, Estevinho MLF, Choupina A. IDENTIFICATION OF HONEY YEAST SPECIES BASED ON RFLP ANALYSIS OF THE ITS REGION IDENTIFICACIÓN DE ESPECIES DE LEVADURAS DE MIEL BASADA EN ANÁLISIS RFLP DE LA REGION ITS IDENTIFICACIÓN DE ESPECIES DE LEVADURAS DE MEL BASADA EN ANÁLISES RFLP DA REXIÓN ITS. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/11358120509487665] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- C. M. Carvalho
- a Departamento de Biologia e Microbiologia , Escola Superior Agrária de Braganç , Apartado 1172, 5301-855, Bragança, Portugal
| | - A. Rocha
- a Departamento de Biologia e Microbiologia , Escola Superior Agrária de Braganç , Apartado 1172, 5301-855, Bragança, Portugal
| | - M. L. F. Estevinho
- a Departamento de Biologia e Microbiologia , Escola Superior Agrária de Braganç , Apartado 1172, 5301-855, Bragança, Portugal
| | - A. Choupina
- a Departamento de Biologia e Microbiologia , Escola Superior Agrária de Braganç , Apartado 1172, 5301-855, Bragança, Portugal
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41
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Ravella SR, James SA, Bond CJ, Roberts IN, Cross K, Retter A, Hobbs PJ. Cryptococcus shivajii sp. nov.: A Novel Basidiomycetous Yeast Isolated from Biogas Reactor. Curr Microbiol 2009; 60:12-6. [DOI: 10.1007/s00284-009-9493-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/21/2009] [Indexed: 11/24/2022]
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42
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Xin G, Glawe D, Doty SL. Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees. ACTA ACUST UNITED AC 2009; 113:973-80. [DOI: 10.1016/j.mycres.2009.06.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 04/03/2009] [Accepted: 06/09/2009] [Indexed: 10/20/2022]
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43
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James SA, Carvajal Barriga EJ, Bond CJ, Cross K, Núñez NC, Portero PB, Roberts IN. Candida carvajalissp. nov., an ascomycetous yeast species from the Ecuadorian Amazon jungle. FEMS Yeast Res 2009; 9:784-8. [DOI: 10.1111/j.1567-1364.2009.00518.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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44
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Chen B, Huang X, Zheng JW, Li SP, He J. Candida mengyuniae sp. nov., a metsulfuron-methyl-resistant yeast. Int J Syst Evol Microbiol 2009; 59:1237-41. [DOI: 10.1099/ijs.0.004614-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Gouliamova D, Dimitrov R, Petrova P, Stoyancheva G, Petrov K. Genomic Approaches to Yeast Taxonomy. BIOTECHNOL BIOTEC EQ 2009. [DOI: 10.1080/13102818.2009.10818477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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46
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Péter G, Tornai-Lehoczki J, Dlauchy D. Candida ogatae sp. nov., an anamorphic member of the Kuraishia clade. FEMS Yeast Res 2008; 9:328-33. [PMID: 19054122 DOI: 10.1111/j.1567-1364.2008.00466.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Three methanol-assimilating yeast strains representing a hitherto undescribed species were isolated from rotten wood and freshwater samples collected in Hungary. Analysis of the D1/D2 large subunit rRNA gene sequences placed the strains in the Kuraishia clade; however, no ascospore formation was observed. These strains differ from Candida hungarica, the genetically most closely related recognized species, by four and five substitutions in D1/D2 and by >1% and 4% differences in the internal transcribed spacer and in the mitochondrial small subunit rRNA gene regions, respectively. Some phenotypic differences were also observed. Candida ogatae, a novel yeast species, is proposed to accommodate these isolates. The type culture is NCAIM Y.01845(T) (CBS 10924, NRRL Y-48474).
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Affiliation(s)
- Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Sciences, Corvinus University of Budapest, Budapest, Hungary.
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47
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MacKenzie DA, Defernez M, Dunn WB, Brown M, Fuller LJ, de Herrera SRMS, Günther A, James SA, Eagles J, Philo M, Goodacre R, Roberts IN. Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics. Yeast 2008; 25:501-12. [PMID: 18615862 DOI: 10.1002/yea.1601] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ten medically important Saccharomyces strains, comprising six clinical isolates of Saccharomyces cerevisiae and four probiotic strains of Saccharomyces boulardii, were characterized at the genetic and metabolic level and compared with non-medical, commercial yeast strains used in baking and wine-making. Strains were compared by genetic fingerprinting using amplified fragment length polymorphism (AFLP) analysis, by ribosomal DNA ITS1 sequencing and by metabolic footprinting using both direct injection mass spectrometry (DIMS) and gas chromatography-time of flight-mass spectrometry (GC-ToF-MS). Overall, the clinical isolates fell into different groupings when compared with the non-medical strains, with good but not perfect correlation amongst strains at both the genetic and metabolic levels. Probiotic strains of S. boulardii that are used therapeutically to treat human gastro-intestinal tract disorders showed tight clustering both genetically and metabolically. Metabolomics was found to be of value both as a taxonomic tool and as a means to investigate anomalous links between genotype and phenotype. Key discriminatory metabolites were identified when comparing the three main groups of clinical, probiotic and non-medical strains and included molecules such as trehalose, myo-inositol, lactic acid, fumaric acid and glycerol 3-phosphate. This study confirmed the link between a subset of clinical isolates and baking or probiotic strains but also highlighted that in general the clinical strains were more diverse at both the genomic and metabolic levels.
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Affiliation(s)
- Donald A MacKenzie
- National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK.
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48
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Solieri L, Giudici P. Yeasts associated to Traditional Balsamic Vinegar: Ecological and technological features. Int J Food Microbiol 2008; 125:36-45. [PMID: 17900732 DOI: 10.1016/j.ijfoodmicro.2007.06.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 06/03/2007] [Accepted: 06/06/2007] [Indexed: 10/22/2022]
Abstract
Traditional Balsamic Vinegar (TBV) is an Italian homemade vinegar made with cooked grape must through a three-step process: conversion of sugars to ethanol by naturally occurring yeasts; oxidation of ethanol to acetic acid by acetic acid bacteria (AAB); and, finally, at least 12-years ageing. The cooked must is a selective and stressful medium for yeasts growth, due to its high sugar content and low pH values. Recent studies have shown that a large number of yeast species are involved in the fermentation, among them there are Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Zygosaccharomyces pseudorouxii, Zygosaccharomyces mellis, Zygosaccharomyces bisporus, Zygosaccharomyces lentus, Hanseniaspora valbyensis, Hanseniaspora osmophila, Candida lactis-condensi, Candida stellata, Saccharomycodes ludwigii and Saccharomyces cerevisiae. Nevertheless, the TBV-associated yeast population could be even more complex and many other slow-growing or poorly cultivable species might contribute to cooked must fermentation. In this review the main TBV yeast species are described, pointing out their role in TBV production and their influence on final product quality. Finally, both future developments in TBV yeast community studies (culture-independent and metagenomic techniques) and technological advances in TBV making (use of starter culture) are discussed.
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Affiliation(s)
- L Solieri
- Department of Agricultural Science, University of Modena and Reggio Emilia, Via J.F. Kennedy 17, 42100 Reggio Emilia, Italy.
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49
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Naumova ES, Serpova EV, Naumov GI. Molecular systematics of Lachancea yeasts. BIOCHEMISTRY (MOSCOW) 2008; 72:1356-62. [PMID: 18205619 DOI: 10.1134/s0006297907120097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This work presents the results of molecular-genetic investigation of a new yeast genus, Lachancea Kurtzman (2003). Analysis of rRNA sequences and molecular karyotyping have shown genetic homogeneity of the genus Lachancea. Yeasts of this genus have an identical haploid number of chromosomes equal to eight, whereas limiting chromosome sizes significantly differ in various species. The largest range of chromosome bands was registered in L. cidri strains (400-2800 kb), while the smallest was found in L. waltii (1400-2800 kb). The intra- and interspecies polymorphism of Lachancea chromosomes is discussed.
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Affiliation(s)
- E S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia
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50
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Bhadra B, Sreenivas Rao R, Naveen Kumar N, Chaturvedi P, Sarkar PK, Shivaji S. Pichia cecembensissp. nov. isolated from a papaya fruit (Carica papaya L., Caricaceae). FEMS Yeast Res 2007; 7:579-84. [PMID: 17316366 DOI: 10.1111/j.1567-1364.2007.00215.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ascogenous yeast YS16T was isolated from a decaying papaya fruit. Phenotypic traits such as multilateral budding, spheroidal or elongate shape, pseudohyphae formation, asci with one or more ascospores, ability to ferment d-glucose, inability to assimilate nitrate and the presence of Q7 ubiquinone suggest its affiliation to the genus Pichia. The nearest phylogenetic neighbor, based on D1/D2 domain sequence of the 26S rRNA gene and ITS region sequence, was identified as Issatchenkia orientalis (NRRL Y-5396T, a synonym of Pichia kudriavzevii) with similarities of 98.2% and 97% respectively. In addition to the difference in the D1/D2 and ITS region sequence, YS16T differs from I. orientalis with respect to a number of phenotypic traits. However, in the phylogenetic analysis, YS16T showed close relatedness to the P. membranifaciens clade. Thus, it is proposed to assign the status of a new species to YS16T, for which the name P. cecembensis sp. nov. is proposed. The type strain of P. cecembensis sp. nov. is YS16T (=NRRL Y-27985T=JCM 13873T=CBS 10445T).
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Affiliation(s)
- Bhaskar Bhadra
- Centre for Cellular and Molecular Biology, Hyderabad, India
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