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Kidd SE, Hagen F, Halliday CL, Abdolrasouli A, Boekhout T, Crous PW, Ellis DH, Elvy J, Forrest GN, Groenewald M, Hahn RC, Houbraken J, Rodrigues AM, Scott J, Sorrell TC, Summerbell RC, Tsui CKM, Yurkov A, Chen SCA. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion. J Clin Microbiol 2024; 62:e0157023. [PMID: 38441055 PMCID: PMC11005369 DOI: 10.1128/jcm.01570-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King’s College Hospital, London, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Teun Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Biology, Molecular Microbiology, Utrecht University, Utrecht, the Netherlands
| | - David H. Ellis
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Juliet Elvy
- Awanui Labs, Dunedin Hospital, Dunedin, New Zealand
| | | | | | - Rosane C. Hahn
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
- Júlio Muller Hospital, EBSERH, Cuiabá, Mato Grosso, Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Anderson M. Rodrigues
- Department of Microbiology, Immunology and Parasitology, Laboratory of Emerging Fungal Pathogens, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - James Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Sporometrics, Toronto, Ontario, Canada
| | - Tania C. Sorrell
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Richard C. Summerbell
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Sporometrics, Toronto, Ontario, Canada
| | - Clement K. M. Tsui
- Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Andrey Yurkov
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
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Makopa TP, Ncube T, Alwasel S, Boekhout T, Zhou N. Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing. Yeast 2024. [PMID: 38450792 DOI: 10.1002/yea.3935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.
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Affiliation(s)
- Tawanda P Makopa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Thembekile Ncube
- Department of Biology and Biochemistry, Faculty of Applied Science, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Brouwer C, Boekhout T, Alwasel S, Rahman M, Janga R, Welling MM. Screening sensibility and antifungal activity after topical application of a synthetic lactoferrin-derived antimicrobial peptide. Am J Transl Res 2024; 16:669-680. [PMID: 38463589 PMCID: PMC10918136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024]
Abstract
OBJECTIVE Onychomycosis is the most common disease of the nails and constitutes about half of all nail abnormalities. Onychomycosis is usually caused by dermatophytes and incomparably less frequently by yeast-like fungi and non-dermatophyte molds. Current treatment options for onychomycosis are ineffective. METHODS This study evaluated the performance of a commercial and CE-registered product containing antimicrobial peptide hLF1-11 in vitro for treating toenail onychomycosis. In a case-control setting, nail samples from 59 volunteers were obtained before and after treatment by a pedicurist and investigated for the presence of fungi by culturing, barcode sequencing, and MALDI-TOF-MS. RESULTS Of 89 samples, T. rubrum (19%) and C. parapsilosis (17%) were cultured. In total, 47 samples (53%) were positive for culture. MALDI-TOF-MS could identify 28, but 19 remained unidentified; those species were not included in the commercial MALDI-TOF reference database library. A positive effect of treatment by the hLF1-11 product on 41 volunteers (1 placebo, 18 low doses, 22 high doses) was observed. No adverse effects of the peptide were observed or reported by the pedicurist or any of the participants. CONCLUSIONS This study showed a positive therapeutic effect of a commercial product containing hLF1-11 in the case of 88.9% of the patients with onychomycosis. The present formulation of hLF1-11 into PBS is stable enough to permit storage at room temperature for at least two years.
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Affiliation(s)
| | - Teun Boekhout
- College of Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Saleh Alwasel
- College of Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | | | - Ruth Janga
- Dushi Pia Medical PedicureIJsselstein, The Netherlands
| | - Mick M Welling
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical CenterLeiden, The Netherlands
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Visagie CM, Meijer M, Kraak B, Groenewald M, Houbraken J, Theelen B, Vorst Y, Boekhout T. Blastobotrys nigripullensis, a new yeast species isolated from a fungal outbreak on an ancient Roman shipwreck in the Netherlands. Antonie Van Leeuwenhoek 2024; 117:22. [PMID: 38217778 DOI: 10.1007/s10482-023-01898-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/08/2023] [Indexed: 01/15/2024]
Abstract
A new species of the yeast genus Blastobotrys was discovered on ancient ship timbers in the Netherlands. The species had developed on the wood of a river barge dating to the Roman period. The growth occurred after the preservative polyethylene glycol (PEG 4000) was washed out of some of the timbers due to an undetected leak in the storage unit. Mycological analysis of various timber samples revealed the presence of Microascus melanosporus (predominant), Microascus paisii, a member of the Acremonium chrysogenum-clade, and a new Blastrobotrys species. The new species produced sporothrix-like conidiophores with clavate blastoconidia (3-7 × 1-3.5 μm) and was found to be osmotolerant, capable of growth on low water activity media like malt yeast 50% glucose agar (MY50G). In this article we formally describe and introduce Blastrobotrys nigripullensis (CBS 17879 T) based on its morphology, physiology and phylogenetic placement.
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Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin Meijer
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | - Bart Kraak
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | | | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | - Yardeni Vorst
- Museumpark Archeon, Restoration Project: Operation Zwammerdam ships, Alphen aan den Rijn, The Netherlands
| | - Teun Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia.
- Retired from Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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Schoutteten N, Yurkov A, Leroux O, Haelewaters D, Van Der Straeten D, Miettinen O, Boekhout T, Begerow D, Verbeken A. Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of Microbotryomycetes. Stud Mycol 2023; 106:41-94. [PMID: 38298570 PMCID: PMC10825749 DOI: 10.3114/sim.2023.106.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/12/2023] [Indexed: 02/02/2024] Open
Abstract
Mycoparasites in Basidiomycota comprise a diverse group of fungi, both morphologically and phylogenetically. They interact with their hosts through either fusion-interaction or colacosome-interaction. Colacosomes are subcellular structures formed by the mycoparasite at the host-parasite interface, which penetrate the parasite and host cell walls. Previously, these structures were detected in 19 fungal species, usually by means of transmission electron microscopy. Most colacosome-forming species have been assigned to Microbotryomycetes (Pucciniomycotina, Basidiomycota), a highly diverse class, comprising saprobic yeasts, mycoparasites, and phytoparasites. In general, these myco- and phytoparasites are dimorphic organisms, with a parasitic filamentous morph and saprobic yeast morph. We investigated colacosome-forming mycoparasites based on fungarium material, freshly collected specimens, and cultures of yeast morphs. We characterised the micromorphology of filamentous morphs, the physiological characteristics of yeast morphs, and inferred phylogenetic relationships based on DNA sequence data from seven loci. We outline and employ an epifluorescence-based microscopic method to assess the presence and organisation of colacosomes. We describe five new species in the genus Colacogloea, the novel dimorphic mycoparasite Mycogloiocolax gerardii, and provide the first report of a sexual, mycoparasitic morph in Colacogloea philyla and in the genus Slooffia. We detected colacosomes in eight fungal species, which brings the total number of known colacosome-forming fungi to 27. Finally, we revealed three distinct types of colacosome organisation in Microbotryomycetes. Taxonomic novelties and typifications: New family: Mycogloiocolacaeae Schoutteten & Yurkov; New genus: Mycogloiocolax Schoutteten & Rödel; New species: Colacogloea bettinae Schoutteten & Begerow, C. biconidiata Schoutteten, C. fennica Schoutteten & Miettinen, C. microspora Schoutteten, C. universitatis-gandavensis Schoutteten & Verbeken, Mycogloiocolax gerardii Schoutteten & Rödel; New combinations: Slooffia micra (Bourdot & Galzin) Schoutteten, Fellozyma cerberi (A.M. Yurkov et al.) Schoutteten & Yurkov, Fellozyma telluris (A.M. Yurkov et al.) Schoutteten & Yurkov; Epitypifications (basionyms): Achroomyces insignis Hauerslev, Platygloea micra Bourdot & Galzin, Platygloea peniophorae Bourdot & Galzin; Lectotypification (basionym): Platygloea peniophorae Bourdot & Galzin Citation: Schoutteten N, Yurkov A, Leroux O, Haelewaters D, Van Der Straeten D, Miettinen O, Boekhout T, Begerow D, Verbeken A (2023). Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of Microbotryomycetes. Studies in Mycology 106: 41-94. doi: 10.3114/sim.2022.106.02.
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Affiliation(s)
- N. Schoutteten
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - A. Yurkov
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - O. Leroux
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - D. Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - D. Van Der Straeten
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - O. Miettinen
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - T. Boekhout
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - D. Begerow
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - A. Verbeken
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
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Del Olmo V, Mixão V, Fotedar R, Saus E, Al Malki A, Księżopolska E, Nunez-Rodriguez JC, Boekhout T, Gabaldón T. Origin of fungal hybrids with pathogenic potential from warm seawater environments. Nat Commun 2023; 14:6919. [PMID: 37903766 PMCID: PMC10616089 DOI: 10.1038/s41467-023-42679-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.
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Affiliation(s)
- Valentina Del Olmo
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Verónica Mixão
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ester Saus
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amina Al Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ewa Księżopolska
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Toni Gabaldón
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
- , Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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Nwaefuna AE, Garcia-Aloy M, Loeto D, Ncube T, Gombert AK, Boekhout T, Alwasel S, Zhou N. Dung beetle-associated yeasts display multiple stress tolerance: a desirable trait of potential industrial strains. BMC Microbiol 2023; 23:309. [PMID: 37884896 PMCID: PMC10601127 DOI: 10.1186/s12866-023-03044-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Stress-tolerant yeasts are highly desirable for cost-effective bioprocessing. Several strategies have been documented to develop robust yeasts, such as genetic and metabolic engineering, artificial selection, and natural selection strategies, among others. However, the significant drawbacks of such techniques have motivated the exploration of naturally occurring stress-tolerant yeasts. We previously explored the biodiversity of non-conventional dung beetle-associated yeasts from extremophilic and pristine environments in Botswana (Nwaefuna AE et.al., Yeast, 2023). Here, we assessed their tolerance to industrially relevant stressors individually, such as elevated concentrations of osmolytes, organic acids, ethanol, and oxidizing agents, as well as elevated temperatures. RESULTS Our findings suggest that these dung beetle-associated yeasts tolerate various stresses comparable to those of the robust bioethanol yeast strain, Saccharomyces cerevisiae (Ethanol Red™). Fifty-six percent of the yeast isolates were tolerant of temperatures up to 42 °C, 12.4% of them could tolerate ethanol concentrations up to 9% (v/v), 43.2% of them were tolerant to formic acid concentrations up to 20 mM, 22.7% were tolerant to acetic acid concentrations up to 45 mM, 34.0% of them could tolerate hydrogen peroxide up to 7 mM, and 44.3% of the yeasts could tolerate osmotic stress up to 1.5 M. CONCLUSION The ability to tolerate multiple stresses is a desirable trait in the selection of novel production strains for diverse biotechnological applications, such as bioethanol production. Our study shows that the exploration of natural diversity in the search for stress-tolerant yeasts is an appealing approach for the development of robust yeasts.
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Affiliation(s)
- Anita Ejiro Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Mar Garcia-Aloy
- Metabolomics Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098, San Michele All'Adige, Italy
| | - Daniel Loeto
- Department of Biological Sciences, University of Botswana, Private Bag, 0022, Gaborone, Botswana
| | - Thembekile Ncube
- Department of Applied Biology and Biochemistry, National University of Science and Technology, P.O. Box AC 939, Ascot, Bulawayo, Zimbabwe
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
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Badiee P, Boekhout T, Zarei Mahmoudabadi A, Mohammadi R, Ayatollahi Mousavi SA, Najafzadeh MJ, Soltani J, Hashemi J, Diba K, Ghadimi-Moghadam A, Salimi-Khorashad AR, Shokohi T, Amin Shahidi M, Ghasemi F, Jafarian H. Erratum for Badiee et al., "Multicenter Study of Susceptibility of Aspergillus Species Isolated from Iranian University Hospitals to Seven Antifungal Agents". Microbiol Spectr 2023; 11:e0225523. [PMID: 37358452 PMCID: PMC10434021 DOI: 10.1128/spectrum.02255-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
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9
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Coelho MA, Ianiri G, David-Palma M, Theelen B, Goyal R, Narayanan A, Lorch JM, Sanyal K, Boekhout T, Heitman J. Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction. Proc Natl Acad Sci U S A 2023; 120:e2305094120. [PMID: 37523560 PMCID: PMC10410736 DOI: 10.1073/pnas.2305094120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining (MAT) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By generating additional chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere-flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight toward the identification of a sexual cycle in Malassezia, with possible implications for pathogenicity.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso86100, Italy
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht3584 CT, The Netherlands
| | - Rohit Goyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
| | - Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
| | - Jeffrey M. Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI53711
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht3584 CT, The Netherlands
- College of Science, King Saud University, Riyadh11451, Saudi Arabia
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
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Vaksmaa A, Polerecky L, Dombrowski N, Kienhuis MVM, Posthuma I, Gerritse J, Boekhout T, Niemann H. Polyethylene degradation and assimilation by the marine yeast Rhodotorula mucilaginosa. ISME Commun 2023; 3:68. [PMID: 37423910 PMCID: PMC10330194 DOI: 10.1038/s43705-023-00267-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023]
Abstract
Ocean plastic pollution is a severe environmental problem but most of the plastic that has been released to the ocean since the 1950s is unaccounted for. Although fungal degradation of marine plastics has been suggested as a potential sink mechanism, unambiguous proof of plastic degradation by marine fungi, or other microbes, is scarce. Here we applied stable isotope tracing assays with 13C-labeled polyethylene to measure biodegradation rates and to trace the incorporation of plastic-derived carbon into individual cells of the yeast Rhodotorula mucilaginosa, which we isolated from the marine environment. 13C accumulation in the CO2 pool during 5-day incubation experiments with R. mucilaginosa and UV-irradiated 13C-labeled polyethylene as a sole energy and carbon source translated to degradation rates of 3.8% yr-1 of the initially added substrate. Furthermore, nanoSIMS measurements revealed substantial incorporation of polyethylene-derived carbon into fungal biomass. Our results demonstrate the potential of R. mucilaginosa to mineralize and assimilate carbon from plastics and suggest that fungal plastic degradation may be an important sink for polyethylene litter in the marine environment.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands.
| | - Lubos Polerecky
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Michiel V M Kienhuis
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Ilsa Posthuma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Jan Gerritse
- Deltares, Unit Subsurface and Groundwater Systems, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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11
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Steins L, Guerreiro MA, Duhamel M, Liu F, Wang QM, Boekhout T, Begerow D. Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales). BMC Genomics 2023; 24:321. [PMID: 37312063 DOI: 10.1186/s12864-023-09387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND The Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilaginales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi. RESULTS In this study, we sequenced genomes of five Pseudozyma species together with six parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate potentially functional mating and meiosis genes that are conserved throughout the whole group. CONCLUSION Our data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.
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Affiliation(s)
- Lena Steins
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
| | - Marco Alexandre Guerreiro
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
- Environmental Genomics, Germany and Max Planck Institute for Evolutionary Biology, Botanical Institute, Christian-Albrechts University of Kiel, Plön, Germany
| | - Marine Duhamel
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Gif-Sur-Yvette, Paris, France
| | - Fei Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany.
- Organismic Botany and Mycology, University of Hamburg, IPM, Hamburg, Germany.
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12
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Coelho MA, Ianiri G, David-Palma M, Theelen B, Goyal R, Narayanan A, Lorch JM, Sanyal K, Boekhout T, Heitman J. Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction. bioRxiv 2023:2023.03.25.534224. [PMID: 36993584 PMCID: PMC10055393 DOI: 10.1101/2023.03.25.534224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining ( MAT ) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By incorporating newly generated chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere- flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight towards the discovery of a sexual cycle in Malassezia , with possible implications for pathogenicity. Significance Statement Malassezia , the dominant fungal group of the mammalian skin microbiome, is associated with numerous skin disorders. Sexual development and yeast-to-hyphae transitions, governed by genes at two mating-type ( MAT ) loci, are thought to be important for fungal pathogenicity. However, Malassezia sexual reproduction has never been observed. Here, we used chromosome-level assemblies and comparative genomics to uncover unforeseen transitions in MAT loci organization within Malassezia , possibly related with fragility of centromeric-associated regions. Additionally, by expressing different MAT alleles in the same cell, we show that Malassezia can undergo hyphal development and this phenotype is associated with increased expression of key mating genes along with other genes known to be virulence factors, providing a possible connection between hyphal development, sexual reproduction, and pathogenicity.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso 86100, Italy
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
| | - Rohit Goyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Jeffrey M. Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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13
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Crous PW, Osieck ER, Shivas RG, Tan YP, Bishop-Hurley SL, Esteve-Raventós F, Larsson E, Luangsa-Ard JJ, Pancorbo F, Balashov S, Baseia IG, Boekhout T, Chandranayaka S, Cowan DA, Cruz RHSF, Czachura P, De la Peña-Lastra S, Dovana F, Drury B, Fell J, Flakus A, Fotedar R, Jurjević Ž, Kolecka A, Mack J, Maggs-Kölling G, Mahadevakumar S, Mateos A, Mongkolsamrit S, Noisripoom W, Plaza M, Overy DP, Piątek M, Sandoval-Denis M, Vauras J, Wingfield MJ, Abell SE, Ahmadpour A, Akulov A, Alavi F, Alavi Z, Altés A, Alvarado P, Anand G, Ashtekar N, Assyov B, Banc-Prandi G, Barbosa KD, Barreto GG, Bellanger JM, Bezerra JL, Bhat DJ, Bilański P, Bose T, Bozok F, Chaves J, Costa-Rezende DH, Danteswari C, Darmostuk V, Delgado G, Denman S, Eichmeier A, Etayo J, Eyssartier G, Faulwetter S, Ganga KGG, Ghosta Y, Goh J, Góis JS, Gramaje D, Granit L, Groenewald M, Gulden G, Gusmão LFP, Hammerbacher A, Heidarian Z, Hywel-Jones N, Jankowiak R, Kaliyaperumal M, Kaygusuz O, Kezo K, Khonsanit A, Kumar S, Kuo CH, Læssøe T, Latha KPD, Loizides M, Luo SM, Maciá-Vicente JG, Manimohan P, Marbach PAS, Marinho P, Marney TS, Marques G, Martín MP, Miller AN, Mondello F, Moreno G, Mufeeda KT, Mun HY, Nau T, Nkomo T, Okrasińska A, Oliveira JPAF, Oliveira RL, Ortiz DA, Pawłowska J, Pérez-De-Gregorio MÀ, Podile AR, Portugal A, Privitera N, Rajeshkumar KC, Rauf I, Rian B, Rigueiro-Rodríguez A, Rivas-Torres GF, Rodriguez-Flakus P, Romero-Gordillo M, Saar I, Saba M, Santos CD, Sarma PVSRN, Siquier JL, Sleiman S, Spetik M, Sridhar KR, Stryjak-Bogacka M, Szczepańska K, Taşkın H, Tennakoon DS, Thanakitpipattana D, Trovão J, Türkekul I, van Iperen AL, van 't Hof P, Vasquez G, Visagie CM, Wingfield BD, Wong PTW, Yang WX, Yarar M, Yarden O, Yilmaz N, Zhang N, Zhu YN, Groenewald JZ. Fungal Planet description sheets: 1478-1549. Persoonia 2023; 50:158-310. [PMID: 38567263 PMCID: PMC10983837 DOI: 10.3767/persoonia.2023.50.05] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/10/2023] [Indexed: 04/04/2024]
Abstract
Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.
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Affiliation(s)
- P W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508AD Utrecht, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - E R Osieck
- Jkvr. C.M. van Asch van Wijcklaan 19, 3972 ST Driebergen-Rijsenburg, Netherlands
| | - R G Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia
| | - Y P Tan
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park 4102, Queensland, Australia
| | - S L Bishop-Hurley
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park 4102, Queensland, Australia
| | - F Esteve-Raventós
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Ciencias de la Vida (Botánica). 28805 Alcalá de Henares, Madrid, Spain
| | - E Larsson
- Biological and Environmental Sciences, University of Gothenburg, and Gothenburg Global Biodiversity Centre, Box 461, SE40530 Göteborg, Sweden
| | - J J Luangsa-Ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - F Pancorbo
- Sociedad Micológica de Madrid, Real Jardín Botánico, C/ Claudio Moyano 1, 28014 Madrid, Spain
| | - S Balashov
- EMSLAnalytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077 USA
| | - I G Baseia
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - T Boekhout
- College of Science, King Saud University, P.O. Box 2455, Riyadh-11451, Saudi Arabia
| | - S Chandranayaka
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore - 570006, Karnataka, India
| | - D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
| | - R H S F Cruz
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, 47810-047, Brazil
| | - P Czachura
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | | | - F Dovana
- Via Quargnento, 17, 15029 Solero, Italy
| | - B Drury
- Queensland College of Teachers, Mount Alvernia College, Kedron 4031, Queensland, Australia
| | - J Fell
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Key Biscayne, Florida, USA
| | - A Flakus
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | - R Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, State of Qatar
| | - Ž Jurjević
- EMSLAnalytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077 USA
| | - A Kolecka
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508AD Utrecht, The Netherlands
| | - J Mack
- Ottawa Research & Development Centre, Agriculture &AgriFood Canada, 960 Carling Ave., Ottawa, Ontario, Canada, K1A 0C6
| | - G Maggs-Kölling
- Gobabeb Namib Research Institute, Walvis Bay, Namibia
- Unit for Environmental Sciences and Management, North-West University, P. Bag X1290, Potchefstroom, 2520, South Africa
| | - S Mahadevakumar
- Forest Pathology Department, Forest Health Division, KSCSTE-Kerala Forest Research Institute, Peechi - 680653, Thrissur, Kerala, India
- Botanical Survey of India, Andaman and Nicobar Regional Center, Haddo - 744102, Port Blair, South Andaman, India
| | - A Mateos
- Sociedad Micológica Extremeña, C/ Sagitario 14, 10001 Cáceres, Spain
| | - S Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - W Noisripoom
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - M Plaza
- C/ La Angostura, 20, 11370 Los Barrios, Cádiz, Spain
| | - D P Overy
- Ottawa Research & Development Centre, Agriculture &AgriFood Canada, 960 Carling Ave., Ottawa, Ontario, Canada, K1A 0C6
| | - M Piątek
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | - M Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508AD Utrecht, The Netherlands
| | - J Vauras
- Biological Collections of Åbo Akademi University, Biodiversity Unit, Herbarium, FI-20014 University of Turku, Finland
| | - M J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - S E Abell
- Australian Tropical Herbarium, James Cook University, Smithfield 4878, Queensland, Australia
| | - A Ahmadpour
- Higher Education Centre of Shahid Bakeri, Urmia University, Miyandoab, Iran
| | - A Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine
| | - F Alavi
- Higher Education Centre of Shahid Bakeri, Urmia University, Miyandoab, Iran
| | - Z Alavi
- Higher Education Centre of Shahid Bakeri, Urmia University, Miyandoab, Iran
| | - A Altés
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Ciencias de la Vida (Botánica). 28805 Alcalá de Henares, Madrid, Spain
| | - P Alvarado
- ALVALAB, Dr. Fernando Bongera st., Severo Ochoa bldg. S1.04, 33006 Oviedo, Spain
| | - G Anand
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) group, MACS Agharkar Research Institute, GG Agharkar Road, Pune, Maharashtra State 411004, India
| | - N Ashtekar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) group, MACS Agharkar Research Institute, GG Agharkar Road, Pune, Maharashtra State 411004, India
| | - B Assyov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria
| | - G Banc-Prandi
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - K D Barbosa
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, 59072-970, Natal, Rio Grande do Norte, Brazil
| | - G G Barreto
- Department of Biology, State University of Feira de Santana, Transnordestina s/n, Novo Horizonte, 44036-900, Feira de Santana, Brazil
| | - J-M Bellanger
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, INSERM, Campus CNRS, 1919 Route de Mende, F-34293 Montpellier, France
| | - J L Bezerra
- Federal University of Pernambuco, Pernambuco, Brazil
| | - D J Bhat
- College of Science, King Saud University, P.O. Box 2455, Riyadh-11451, Saudi Arabia
| | - P Bilański
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - T Bose
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F Bozok
- Department of Biology, Faculty ofArts and Science, Osmaniye KorkutAta University, 80000 Osmaniye, Türkiye
| | - J Chaves
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Diego de Robles s/n, 170901, Quito, Ecuador
- San Francisco State University, Department of Biology, 1600 Holloway Av, San Francisco CA 94132, USA
| | - D H Costa-Rezende
- Department of Biology, State University of Feira de Santana, Transnordestina s/n, Novo Horizonte, 44036-900, Feira de Santana, Brazil
| | - C Danteswari
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - V Darmostuk
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | - G Delgado
- Eurofins Built Environment, 6110 W. 34th St, Houston, TX 77092, USA
| | - S Denman
- Forest Research, Alice Holt Lodge, Farnham, Surrey, UK
| | - A Eichmeier
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, Lednice, 69144, Czech Republic
| | - J Etayo
- Navarro Villoslada 16, 3º cha., E-31003 Pamplona, Navarra, Spain
| | - G Eyssartier
- Institut de systématique, évolution, biodiversité (UMR 7205-MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles), 45 rue Buffon, F-75005 Paris, France
| | - S Faulwetter
- Department of Geology, University of Patras, 26504 Rio Patras, Greece
| | - K G G Ganga
- Department of Botany, University of Calicut, Kerala, 673 635, India
| | - Y Ghosta
- Department of Plant Protection, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - J Goh
- Fungal Research Team, Microbial Research Department, Nakdonggang National Institute of Biological Resources, Korea
| | - J S Góis
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, 59072-970, Natal, Rio Grande do Norte, Brazil
| | - D Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, 26007 Logroño, Spain
| | - L Granit
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel & Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - M Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508AD Utrecht, The Netherlands
| | - G Gulden
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
| | - L F P Gusmão
- Department of Biology, State University of Feira de Santana, Transnordestina s/n, Novo Horizonte, 44036-900, Feira de Santana, Brazil
| | - A Hammerbacher
- Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - Z Heidarian
- Higher Education Centre of Shahid Bakeri, Urmia University, Miyandoab, Iran
| | - N Hywel-Jones
- Zhejiang BioAsia Institute of Life Sciences, Pinghu 314200, Zhejiang, People's Republic of China
| | - R Jankowiak
- Department of Forest Ecosystems Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - M Kaliyaperumal
- CAS in Botany, University of Madras, Chennai, Tamil Nadu, India
| | - O Kaygusuz
- Department of Plant and Animal Production, Atabey Vocational School, Isparta University of Applied Sciences, 32670 Isparta, Türkiye
| | - K Kezo
- CAS in Botany, University of Madras, Chennai, Tamil Nadu, India
| | - A Khonsanit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - S Kumar
- Forest Pathology Department, Forest Health Division, KSCSTE-Kerala Forest Research Institute, Peechi - 680653, Thrissur, Kerala, India
| | - C H Kuo
- Department of Plant Medicine, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - T Læssøe
- Globe Institute/Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - K P D Latha
- Department of Botany, University of Calicut, Kerala, 673 635, India
| | | | - S M Luo
- University of Sydney, Plant Breeding Institute, 107 Cobbitty Rd, Cobbitty, New South Wales, Australia
| | - J G Maciá-Vicente
- Plant Ecology and Nature Conservation, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, The Netherlands
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - P Manimohan
- Department of Botany, University of Calicut, Kerala, 673 635, India
| | - P A S Marbach
- Recôncavo da Bahia Federal University, Bahia, Brazil
| | - P Marinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - T S Marney
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park 4102, Queensland, Australia
| | - G Marques
- CITAB-University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - M P Martín
- Departamento de Micología, Real Jardín Botánico RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - A N Miller
- University of Illinois Urbana-Champaign, Illinois Natural History Survey, 1816 South Oak Street, Champaign, Illinois, 61820, USA
| | - F Mondello
- Via B. da Neocastro, 26, 98123 Messina, Italy
| | - G Moreno
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Ciencias de la Vida (Botánica). 28805 Alcalá de Henares, Madrid, Spain
| | - K T Mufeeda
- Forest Pathology Department, Forest Health Division, KSCSTE-Kerala Forest Research Institute, Peechi - 680653, Thrissur, Kerala, India
| | - H Y Mun
- Fungal Research Team, Microbial Research Department, Nakdonggang National Institute of Biological Resources, Korea
| | - T Nau
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - T Nkomo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A Okrasińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - R L Oliveira
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, 59072-970, Natal, Rio Grande do Norte, Brazil
| | - D A Ortiz
- Universidad San Francisco de Quito USFQ, Galapagos Science Center GSC, San Cristóbal 200101, Galápagos, Ecuador
| | - J Pawłowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - A R Podile
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - A Portugal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3004-531 Coimbra, Portugal
- Fitolab - Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - N Privitera
- Associazione Micologica Bresadola Gruppo di Catania, Via Macallè 18, I-95125 Catania, Italy
| | - K C Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) group, MACS Agharkar Research Institute, GG Agharkar Road, Pune, Maharashtra State 411004, India
| | - I Rauf
- Department of Plant Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - B Rian
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
| | | | - G F Rivas-Torres
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Diego de Robles s/n, 170901, Quito, Ecuador
- Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Universidad San Francisco de Quito USFQ, Galapagos Science Center GSC, San Cristóbal 200101, Galápagos, Ecuador
| | - P Rodriguez-Flakus
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | | | - I Saar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi Street 2, 50409 Tartu, Estonia
| | - M Saba
- Department of Plant Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - C D Santos
- Federal Institute of the Sertão Pernambucano, Pernambuco, Brazil
| | - P V S R N Sarma
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - J L Siquier
- Interdisciplinary Ecology Group, University of the Balearic Islands, crtra. to Valldemossa km 7.5, 07122 Mallorca, Spain
| | - S Sleiman
- Project Manager, Council of Environment, Akkar, North Lebanon
| | - M Spetik
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, Lednice, 69144, Czech Republic
| | - K R Sridhar
- Department of Biosciences, Mangalore University, Mangalagangotri, Mangalore - 574199, Karnataka, India
| | - M Stryjak-Bogacka
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
| | - K Szczepańska
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, pl. Grunwaldzki 24a, PL-50-363 Wrocław, Poland
| | - H Taşkın
- Department of Horticulture, Faculty of Agriculture, Cukurova University, 01330 Adana, Türkiye
| | - D S Tennakoon
- Faculty of Science, Department of Biology, Chiang Mai University, 50200, Chiang Mai, Thailand
| | - D Thanakitpipattana
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - J Trovão
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3004-531 Coimbra, Portugal
| | - I Türkekul
- Department of Biology, Faculty of Science and Arts, Gaziosmanpaşa University, 60010 Tokat, Türkiye
| | - A L van Iperen
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508AD Utrecht, The Netherlands
| | - P van 't Hof
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Diego de Robles s/n, 170901, Quito, Ecuador
- Universidad San Francisco de Quito USFQ, Galapagos Science Center GSC, San Cristóbal 200101, Galápagos, Ecuador
| | - G Vasquez
- Department of Biology, Geology and Environmental Science, University of Catania, Via A. Longo 19, I-95125 Catania, Italy
| | - C M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - B D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P T W Wong
- University of Sydney, Plant Breeding Institute, 107 Cobbitty Rd, Cobbitty, New South Wales, Australia
| | - W X Yang
- College of Plant Protection, Hebei Agricultural University, 289 Lingyusi Street, Baoding, Hebei Province, China
| | - M Yarar
- Department of Biotechnology, Institute of Natural and Applied Sciences, Cukurova University, 01330 Adana, Türkiye
| | - O Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel & Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - N Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - N Zhang
- College of Plant Protection, Hebei Agricultural University, 289 Lingyusi Street, Baoding, Hebei Province, China
| | - Y N Zhu
- College of Plant Protection, Hebei Agricultural University, 289 Lingyusi Street, Baoding, Hebei Province, China
| | - J Z Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508AD Utrecht, The Netherlands
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14
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Mixão V, Nunez-Rodriguez JC, Del Olmo V, Ksiezopolska E, Saus E, Boekhout T, Gacser A, Gabaldón T. Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens. BMC Biol 2023; 21:105. [PMID: 37170256 PMCID: PMC10173528 DOI: 10.1186/s12915-023-01608-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the high levels of genetic heterozygosity present in hybrids from divergent parents are likely to result in numerous deleterious epistatic interactions. Under this scenario, selection is expected to favor recombination events resulting in loss of heterozygosity (LOH) affecting genes involved in such negative interactions. Nevertheless, it is so far unknown whether this phenomenon actually drives genomic evolution in natural populations of hybrids. To determine the balance between selection and drift in the evolution of LOH patterns in natural yeast hybrids, we analyzed the genomic sequences from fifty-five hybrid strains of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis, which derived from at least six distinct natural hybridization events. RESULTS We found that, although LOH patterns in independent hybrid clades share some level of convergence that would not be expected from random occurrence, there is an apparent lack of strong functional selection. Moreover, while mitosis is associated with a limited number of inter-homeologous chromosome recombinations in these genomes, induced DNA breaks seem to increase the LOH rate. We also found that LOH does not accumulate linearly with time in these hybrids. Furthermore, some C. orthopsilosis hybrids present LOH patterns compatible with footprints of meiotic recombination. These meiotic-like patterns are at odds with a lack of evidence of sexual recombination and with our inability to experimentally induce sporulation in these hybrids. CONCLUSIONS Our results suggest that genetic drift is the prevailing force shaping LOH patterns in these hybrid genomes. Moreover, the observed LOH patterns suggest that these are likely not the result of continuous accumulation of sporadic events-as expected by mitotic repair of rare chromosomal breaks-but rather of acute episodes involving many LOH events in a short period of time.
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Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Present address: Genomics and Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE "Lendület" Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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15
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Nwaefuna AE, Boekhout T, Garcia-Aloy M, Vrhovsek U, Zhou N. Diversity of dung beetle-associated yeasts from pristine environments of Botswana. Yeast 2023. [PMID: 37096317 DOI: 10.1002/yea.3852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/26/2023] Open
Abstract
Yeast-insect interactions are increasingly becoming an attractive source of discovery for previously unknown, unique, diverse, and industrially relevant yeast species. Despite a wealth of studies that have recently focused on yeasts in symbiotic association with Hymenopteran insects, yeasts associated with Coleopteran insects, such as lignocellulosic-rich dung-dependent beetles, remain poorly studied. Trends in yeast discovery suggest that species richness and diversity can be attributed to the ecological niche of the insect. Here, we considered the potential of dung beetles inhabiting the extreme environments of Botswana, characterized by desert-like conditions (semi-arid to arid and hot) as well as protected pristine environments, as possible attribute niches that can shape the extremophilic and diverse life history strategies of yeasts. We obtained a total of 97 phylogenetically diverse yeast isolates from six species of dung beetles from Botswana's unexplored environments, representing 19 species belonging to 11 genera. The findings suggest that the guts of dung beetles are a rich niche for non-Saccharomyces yeast species. Meyerozyma and Pichia were the most dominant genera associated with dung beetles, representing 55% (53 out of 97) of the yeast isolates in our study. Trichosporon and Cutaneotrichosporon genera represented 32% (31 out of 97) of the isolates. The remaining isolates belonged to Apiotrichum, Candida, Diutina, Naganishia, Rhodotorula, and Wickerhamiella genera (12 out of 97). We found out that about 62% (60 out of 97) of the isolates were potentially new species because of their low internal transcribed spacer (ITS) sequence similarity when compared to the most recent optimal species delineation threshold. A single isolate was unidentifiable using the ITS sequences. Using an in silico polymerase chain reaction-restriction fragment length polymorphism approach, we revealed that there was genetic diversity within isolates of the same species. Our results contribute to the knowledge and understanding of the diversity of dung beetle-associated yeasts.
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Affiliation(s)
- Anita E Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Teun Boekhout
- Westerdijk Institute of Fungal Biodiversity, Utrecht, The Netherlands
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mar Garcia-Aloy
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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16
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Christinaki AC, Theelen B, Zania A, Coutinho SDA, Cabañes JF, Boekhout T, Kouvelis VN. Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia. Sci Rep 2023; 13:6308. [PMID: 37072481 PMCID: PMC10113387 DOI: 10.1038/s41598-023-33486-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.
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Affiliation(s)
- Anastasia C Christinaki
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Alkmini Zania
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | | | - Javier F Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece.
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17
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Hawaz E, Tafesse M, Tesfaye A, Kiros S, Beyene D, Kebede G, Boekhout T, Groenwald M, Theelen B, Degefe A, Degu S, Admasu A, Hunde B, Muleta D. Optimization of bioethanol production from sugarcane molasses by the response surface methodology using Meyerozyma caribbica isolate MJTm3. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-022-01706-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Abstract
Purpose
Yeast strains tolerant to a wide range of stress conditions are needed for the production of bioethanol from substrates rich in sugar. In our earlier research findings, Meyerozyma caribbica isolate MJTm3 (OM329077) demonstrated remarkable stress tolerance and fermentative activity. The present study aimed to optimize six fermentation parameters to generate conducive fermentation conditions for ethanol production by M. caribbica isolate MJTm3.
Method
The response surface method (RSM) based on central composite design (CCD) was employed to optimize process conditions for higher bioethanol yield. The optimization process was carried out based on six independent parameters, namely temperature (25–35 °C), pH (5.5–6.5), inoculum size (10–20% (v/v)), molasses concentration (25–35 (w/v)), mixing rate (110–150 rpm), and incubation period (48–72-h). Analysis of ethanol concentration was done by HPLC equipped with a UV detector.
Result
The optimal conditions of the parameters resulting in a maximum predicted ethanol yield were as follows: pH 5.5, an inoculum size of 20%, a molasses concentration of 25 °Bx, a temperature of 30 °C, an incubation period of 72-h, and a mixing rate of 160 revolutions per minute (rpm). Using the above optimum conditions, the model predicted a bioethanol yield of 79%, 92% of the theoretical yield, a bioethanol concentration of 49 g L−1, and a productivity of 0.68 g L−1 h−1. A batch fermentation experiment was carried out to validate the predicted values and resulted in a bioethanol yield of 86%, 95% of theoretical yield, a bioethanol concentration of 56 g L−1, and productivity of 0.78 g L−1 h−1. On the other hand, the surface plot analysis revealed that the synergistic effect of the molasses concentration and the mixing rate were vital to achieving the highest bioethanol yield. These values suggested that the RSM with CCD was an effective method in producing the highest possible output of bioethanol from molasses in actual operation.
Conclusion
The study confirmed the potential of using M. caribbica isolate MJTm3 for bioethanol production from sugarcane molasses under the abovementioned optimal fermentation conditions.
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18
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Salah H, Houbraken J, Boekhout T, Almaslamani M, Taj-Aldeen SJ. Molecular epidemiology of clinical filamentous fungi in Qatar beyond Aspergillus and Fusarium with notes on the rare species. Med Mycol 2023; 61:6967136. [PMID: 36592959 PMCID: PMC9874029 DOI: 10.1093/mmy/myac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/12/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Due to an increasing number of patients at risk (i.e., those with a highly compromised immune system and/or receiving aggressive chemotherapy treatment), invasive fungal infections (IFI) are increasingly being reported and associated with high mortality rates. Aspergillus spp., particularly A. fumigatus, is the major cause of IFI caused by filamentous fungi around the world followed by Fusarium spp., however, other fungi are emerging as human pathogens. The aim of this study was to explore the epidemiology and prevalence of the non-Aspergillus and non-Fusarium filamentous fungi in human clinical samples over an 11-year period in Qatar using molecular techniques. We recovered 53 filamentous fungal isolates from patients with various clinical conditions. Most patients were males (75.5%), 9.4% were immunocompromised, 20.7% had IFI, and 11.3% died within 30 days of diagnosis. The fungal isolates were recovered from a variety of clinical samples, including the nasal cavity, wounds, respiratory samples, body fluids, eye, ear, tissue, abscess, and blood specimens. Among the fungi isolated, 49% were dematiaceous fungi, followed by Mucorales (30%), with the latter group Mucorales being the major cause of IFI (5/11, 45.5%). The current study highlights the epidemiology and spectrum of filamentous fungal genera, other than Aspergillus and Fusarium, recovered from human clinical samples in Qatar, excluding superficial infections, which can aid in the surveillance of uncommon and emerging mycoses.
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Affiliation(s)
- Husam Salah
- To whom correspondence should be addressed. Husam Salah, M.Sc. Division
of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical
Corporation, Doha, Qatar, PO Box 3050. Tel: +97-444-391-047. E-mail: ;
| | - Jos Houbraken
- Applied and Industrial Mycology, Westerdijk Fungal Biodiversity
Institute, Utrecht, Netherlands
| | - Teun Boekhout
- Yeast Research, Westerdijk Fungal Biodiversity Institute,
Utrecht, Netherlands,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of
Amsterdam, Amsterdam, The
Netherlands
| | | | - Saad J Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and
Pathology, Hamad Medical Corporation, Doha,
Qatar,Department of Biology, College of Science, University of
Babylon, Hilla, Iraq
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19
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Visagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast 2023; 40:7-31. [PMID: 36168284 PMCID: PMC10108157 DOI: 10.1002/yea.3816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 01/18/2023] Open
Abstract
A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.
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Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Neriman Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Keith A Seifert
- Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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20
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Gringhuis SI, Kaptein TM, Remmerswaal EBM, Drewniak A, Wevers BA, Theelen B, D'Haens GRAM, Boekhout T, Geijtenbeek TBH. Fungal sensing by dectin-1 directs the non-pathogenic polarization of T H17 cells through balanced type I IFN responses in human DCs. Nat Immunol 2022; 23:1735-1748. [PMID: 36456734 DOI: 10.1038/s41590-022-01348-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/29/2022] [Indexed: 12/05/2022]
Abstract
The non-pathogenic TH17 subset of helper T cells clears fungal infections, whereas pathogenic TH17 cells cause inflammation and tissue damage; however, the mechanisms controlling these distinct responses remain unclear. Here we found that fungi sensing by the C-type lectin dectin-1 in human dendritic cells (DCs) directed the polarization of non-pathogenic TH17 cells. Dectin-1 signaling triggered transient and intermediate expression of interferon (IFN)-β in DCs, which was mediated by the opposed activities of transcription factors IRF1 and IRF5. IFN-β-induced signaling led to integrin αvβ8 expression directly and to the release of the active form of the cytokine transforming growth factor (TGF)-β indirectly. Uncontrolled IFN-β responses as a result of IRF1 deficiency induced high expression of the IFN-stimulated gene BST2 in DCs and restrained TGF-β activation. Active TGF-β was required for polarization of non-pathogenic TH17 cells, whereas pathogenic TH17 cells developed in the absence of active TGF-β. Thus, dectin-1-mediated modulation of type I IFN responses allowed TGF-β activation and non-pathogenic TH17 cell development during fungal infections in humans.
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Affiliation(s)
- Sonja I Gringhuis
- Department of Experimental Immunology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands. .,Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands.
| | - Tanja M Kaptein
- Department of Experimental Immunology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Ester B M Remmerswaal
- Department of Experimental Immunology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands.,Renal Transplant Unit, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Agata Drewniak
- Department of Experimental Immunology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Brigitte A Wevers
- Department of Experimental Immunology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Geert R A M D'Haens
- Gastroenterology and Hepatology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands. .,Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands.
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21
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Hawaz E, Tafesse M, Tesfaye A, Beyene D, Kiros S, Kebede G, Boekhout T, Theelen B, Groenewald M, Degefe A, Degu S, Admas A, Muleta D. Isolation and characterization of bioethanol producing wild yeasts from bio-wastes and co-products of sugar factories. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01695-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Yeasts are widely used for the production of bioethanol from biomasses rich in sugar. The present study was aimed at isolating, screening, and characterizing fermentative wild yeast recovered from bio-waste and co-products of Ethiopian sugar factories for bioethanol production using sugarcane molasses as a substrate.
Method
The wild yeasts were identified according to their cellular morphology and D1/D2 and ITS1-5.8S-ITS2 rDNA sequencing. Analysis of ethanol and by-product concentration was done by HPLC equipped with a UV detector. Higher alcohols, acetaldehyde, and methanol were analyzed using GC-MS equipped with a flame ionization detector (FID).
Result
Seven strains (Meyerozyma caribbica MJTm3, Meyerozyma caribbica MJTPm4, Meyerozyma caribbica SHJF, Saccharomyces cerevisiae TA2, Wickerhamomyces anomalus MJTPm2, Wickerhamomyces anomalus 4m10, and Wickerhamomyces anomalus HCJ2F) were found tolerant to 18% (v/v) ethanol, whereas one strain Meyerozyma caribbica MJTm3 tolerated 20%. These strains also showed tolerance to 45°C, 50% of sugar, and pH 2–10. Meyerozyma caribbica MJTm3 produced 12.7% (v/v) of alcohol with an actual ethanol concentration of 26 g L−1, an ethanol yield of 47%, 78% of theoretical yield, and a productivity of 0.54 g L−1 h−1 from 30 °Brix of molasses at 48 h incubation under laboratory scale. Based on the one variable at a time optimization (OVAT), the optimal parameters for maximum bioethanol production were at initial pH 5.5, 35 °Brix, 30°C, 15% inoculum size, 150 rpm, 4 g L−1 di-ammonium phosphate supplement, and 48 h incubation. Under these optimum conditions, 14% (v/v) alcohol, 42 g L−1 actual ethanol concentration, 69% ethanol yield, 89% of theoretical yield, and productivity of 0.88 g L−1 h−1 were obtained.
Conclusion
These results indicated that M. caribbica MJTm3 should further be evaluated, optimized, and improved for industrial bioethanol production due to its fermentation potential.
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22
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Khodavaisy S, Kord M, Elmimoghaddam A, Hashemi SJ, Reziae S, Ghazvini RD, Salehi M, Abdollahi A, Ahmadi A, Boekhout T. P402 Comparison of PCR-RFLP with 21-plex PCR and rDNA: sequencing for identification of clinical yeast isolates. Med Mycol 2022. [PMCID: PMC9509755 DOI: 10.1093/mmy/myac072.p402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM
Objectives
Non-albicans Candida species and other rare yeasts have emerged as major opportunistic pathogens in fungal infections. Identification of opportunistic yeasts in developing countries is mainly performed by phenotypic assay, which is time-consuming and prone to errors. The aim of the present study was to evaluate PCR-RFLP as a routinely used identification technique for the most clinically important Candida species in Iran and make a comparison with a novel multiplex PCR, called 21-plex PCR.
Methods
A total of 173 yeast isolates from clinical sources were selected and identified with sequence analysis of the D1/D2 domains of rDNA (LSU rDNA) sequencing as the gold standard method.
Results
The results were compared with those obtained by PCR-RFLP using MspI restriction enzyme and the 21-plex PCR. PCR-RFLP correctly identified 93.4% of common pathogenic Candida species (C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and P. kudriavsevii (=C. krusei)) and was able to identify 45.5% of isolates of the uncommon yeast species compared to the D1/D2 rDNA sequencing. Compared with PCR RFLP, all common Candida species and 72.7% of uncommon yeast species were correctly identified by the 21-plex PCR.
Conclusion
The application of the 21-plex PCR assay as a non-sequence-based molecular method for the identification of common and rare yeasts can reduce turnaround time and costs for the identification of clinically important yeasts and can be applied in resource-limited settings.
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Affiliation(s)
- Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Mohammad Kord
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Ahmad Elmimoghaddam
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Seyed Jamal Hashemi
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Sassan Reziae
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Roshanak Daie Ghazvini
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran , Iran
| | - Alireza Abdollahi
- Department of Pathology , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran , Iran
| | - Ali Ahmadi
- Department of Medical Parasitology and Mycology , School of Public Health, Tehran University of Medical Sciences, Tehran , Iran
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
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23
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Mohamed HE, Houbraken J, Boekhout T, Almaslaman M, Taj-Aldeen S. P276 Molecular epidemiology of clinical filamentous fungi in Qatar beyond Aspergillus and Fusarium. Med Mycol 2022. [PMCID: PMC9509984 DOI: 10.1093/mmy/myac072.p276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM
Objectives
Due to an increasing number of patients at risk, (ie, with a highly compromised immune system and/or receiving aggressive chemotherapy treatment), invasive fungal infections (IFI) are increasingly being reported. They are associated with significantly high mortality rates. Aspergillus spp., particularly A. fumigatus, is the major cause of mold-related IFI around the world followed by Fusarium spp., however, other molds are emerging as human pathogens. The aim of this study was to explore the epidemiology and prevalence of the non-Aspergillus and non-Fusarium molds in human clinical samples over 11 years period in Qatar based tertiary hospital using molecular techniques.
Methods
A total of 91 clinical specimens positive for molds belonging to 90 patients were recorded in about 11 years (September 2003 to November 2014). The isolates were identified based on morphological characteristics and by sequencing the internal transcribed spacer (ITS) gene. To confirm the identifications, a phylogenetic tree based on ITS sequences was constructed.
Results
Most patients were males (72%), 6% were immunocompromised, 12% had IFI, and 7% died within 30 days of diagnosis. The fungal isolates were recovered from a variety of clinical samples, including nails, skin, hair, scalp, nasal cavity, wounds, respiratory samples, body fluids, eye, ear, tissue, abscess, and blood specimens. Dematiaceous fungi were overall the most isolated (33/91, 36%), followed by dermatophytes (25/91, 27%), Mucorales (16/91, 18%), and other hyaline molds (17/91, 19%) (Fig. 1). Curvularia was the most isolated genus (22/91, 24%) and Mucorales were the major cause of IF (5/11, 45.5%) (Table 1). Superficial mycoses were caused by dermatophytes (66%) and non-dermatophytes (34%). Furthermore, rare fungi that are not commonly known to cause human disease were recovered such as Rhytidhysteron rufulum, Subramaniula asteroids, Dothichiza pimprina, and Quambalaria cyanescens.
Conclusion
The current study highlights the epidemiology and spectrum of mold genera, other than Aspergillus and Fusarium, recovered from human clinical samples in Qatar, which can aid in surveillance of uncommon and emerging mycoses other than aspergillosis and fusuriosis.
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Affiliation(s)
- Husam Eldin Mohamed
- Division of Microbiology , Department of Laboratory Medicine and Pathology, Hamad Medical Corporation., Doha , Qatar
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED) , University of Amsterdam, Amsterdam , The Netherlands
| | | | - Saad Taj-Aldeen
- Division of Microbiology , Department of Laboratory Medicine and Pathology, Hamad Medical Corporation., Doha , Qatar
- University of Babylon , Hilla , Iraq
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24
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Taj-Aldeen S, Francisco E, Al Maslamani M, Theelen B, Vu D, Boekhout T, Hagen F. P490 Fatal secondary fungemia due to Trichosporon asahii onychomycosis in a diabetic patient. Med Mycol 2022. [PMCID: PMC9509946 DOI: 10.1093/mmy/myac072.p490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM Objectives We describe a fatal case of trichosporonosis caused by Trichosporon asahii. The aim was to molecularly characterize the T. asahii strains from blood and foot tissue samples to investigate their genetic relatedness. Case An 85-year-old morbidly obese female with a prior cerebrovascular accident, hypertension, and diabetes mellitus was admitted to a peripheral hospital with type II respiratory failure, metabolic acidosis, and chronic anemia. Three weeks post-hospitalization the patient remained febrile, physical examination showed that the patient had paronychia, nail pigmentation, subungual onychomycosis, and a diabetic foot ulcer. Blood culture, as well as nail and ulcer samples, became positive for Trichosporon yeasts. Methods Trichosporon yeasts were subjected to molecular identification by sequencing the intergenic spacer (IGS1) region. Minimal inhibitory concentrations (MICs) were determined by the EUCAST microdilution method. Long-read nanopore sequencing was performed for the three clinical strains, the type-strain of T. asahii (CBS2479), and two IGS-genotype 7 strains (CBS2936, CBS7632) using the native barcoding kit v12 (SQK-LSK112; Oxford Nanopore Technologies). Raw data were basecalled with Guppy v6, Flye v2.9 was used to de novo assemble the genome of CBS2479, this was used as a reference for variant calling using the genomic reads of all strains. Results The three clinical strains were found to belong to the rare IGS-genotype 7 and had similar MICs for amphotericin B (4 µg/ml), 5-fluorocytosine and fluconazole (2 µg/ml), voriconazole (≤ 0.015 µg/ml), posaconazole (0.0625 µg/ml), itraconazole (0.125 µg/ml), caspofungin (8 µg/ml), anidulafungin and micafungin (> 16 µg/ml). Strains from the ulcer and nail were genetically very closely related with 10 836 SNPs differences, the blood-derived strain differed more from these two strains with 94 729 SNPs and 94 913 SNPs, respectively. Strains CBS2936 and CBS7632 were only distantly related to CBS2479 with 328 221, and 436 060 SNPs, respectively. Conclusion The T. Asahii IGS-genotype 7 strain causing fatal fungemia was genetically nearly identical to that obtained from nail and foot ulcers, making it highly likely that this was the port d'entrée for T. asahii.
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Affiliation(s)
- Saad Taj-Aldeen
- Mycology Laboratory , Department of Medicine and Pathology, Hamad Medical Corporation, Doha , Qatar
- University of Babylon , Hilla , Iraq
| | - Elaine Francisco
- Division of Infectious Diseases , Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo , Brazil
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
| | - Muna Al Maslamani
- Infectious Diseases , Hamad Medical Corporation, Communicable Diseases Centre, Doha , Qatar
- Weill Cornell Medicine , Doha , Qatar
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED) , University of Amsterdam, Amsterdam , The Netherlands
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED) , University of Amsterdam, Amsterdam , The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute , Utrecht , The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED) , University of Amsterdam, Amsterdam , The Netherlands
- Department of Medical Microbiology , University Medical Center Utrecht, Utrecht , The Netherlands
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25
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Badiee P, Boekhout T, Zarei Mahmoudabadi A, Mohammadi R, Ayatollahi Mousavi SA, Najafzadeh MJ, Soltani J, Hashemi J, Diba K, Ghadimi-Moghadam A, Salimi-Khorashad AR, Shokohi T, Amin Shahidi M, Ghasemi F, Jafarian H. Multicenter Study of Susceptibility of Aspergillus Species Isolated from Iranian University Hospitals to Seven Antifungal Agents. Microbiol Spectr 2022; 10:e0253921. [PMID: 35579442 PMCID: PMC9241793 DOI: 10.1128/spectrum.02539-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/17/2022] [Indexed: 12/24/2022] Open
Abstract
Aspergillus species are a major cause of life-threatening invasive infections and noninvasive diseases. This study seeks to investigate the frequency of Aspergillus species among Iranian patients and their susceptibility to seven antifungals. In a cross-sectional study, 233 Aspergillus isolates were collected from 11 university hospitals in Iran between 2018 and 2021. Aspergillus isolates were identified based on colony morphology, microscopic characteristics, PCR-restriction fragment length polymorphism (RFLP), and sequencing of the beta-tubulin gene. The CLSI M38-A2 reference methodology was used for antifungal susceptibility testing of amphotericin B, voriconazole, posaconazole, itraconazole, luliconazole, isavuconazole, and caspofungin. Members of Aspergillus section Flavi (117/233, 50.2%), Aspergillus section Nigri (77/233, 33.1%), Aspergillus section Fumigati (21/233, 9%), Aspergillus section Terrei (14/233, 6%), Aspergillus pseudodeflectus (2/233, 0.85%), and Aspergillus melleus (2/233, 0.85%) were isolated from the samples. The lowest 0.25 MIC90 values for all isolates tested were for luliconazole (0.016 μg/mL) and isavuconazole (0.250 μg/mL), and the highest value was observed for itraconazole (≥ 8μg/mL). The 90% minimum effective concentration (MEC90) value for caspofungin was 0.125 μg/mL. MIC90 values for voriconazole, amphotericin B, and posaconazole were 1, 2, and 2 μg/mL, respectively. The non-wild-type species were presented for amphotericin B (3%), voriconazole (1.3%), posaconazole (2.6%), luliconazole (1.3%), isavuconazole (1.7%), and caspofungin (4.7%). Positive correlations in the MIC values of azole antifungals were observed, and using one azole increases the MIC value rates of other ones. None of the species were pan-azole resistant. Species of Aspergillus section Flavi were the most common Aspergillus species isolated from Iranian samples. Luliconazole, caspofungin, and isavuconazole present the most effective antifungal agents for treatment of infection due to Aspergillus species. Susceptibility tests should be performed frequently in each region for the best management of patients. IMPORTANCE Aspergillus species are the leading cause of invasive aspergillosis in immunocompromised hosts. The susceptibility of Aspergillus species to antifungal agents might be different. Azole-resistant species have emerged worldwide. Performing susceptibility testing in each region can help in the best management of patients. Here, we show the epidemiology and distribution of Aspergillus species in Iran and their susceptibility patterns for seven antifungal agents. The significant points of the present study are that species of Aspergillus section Flavi are the most prevalent Aspergillus species isolated from 11 university hospitals. Luliconazole, caspofungin, and isavuconazole were effective antifungal agents against all Aspergillus species.
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Affiliation(s)
- Parisa Badiee
- Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - Ali Zarei Mahmoudabadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Rasoul Mohammadi
- Department of Medical Parasitology and Mycology, School of Medicine, Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyyed Amin Ayatollahi Mousavi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Javad Najafzadeh
- Department of Medical Parasitology and Mycology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jafar Soltani
- Department of Pediatrics, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Jamal Hashemi
- Medical Mycology Department, School of Public Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Kambiz Diba
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Abdolkarim Ghadimi-Moghadam
- Department of Pediatrics Infectious Disease, Emmam Sajjad Hospital, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Ali Reza Salimi-Khorashad
- Department of Parasitology and Mycology, School of Medicine, Infectious Diseases and Tropical Medicine Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Tahereh Shokohi
- Department of Medical Mycology, School of Medicine, Invasive Fungi Research Centre (IFRC), Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maneli Amin Shahidi
- Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Ghasemi
- Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hadis Jafarian
- Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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26
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Christinaki AC, Kanellopoulos SG, Kortsinoglou AM, Andrikopoulos MΑ, Theelen B, Boekhout T, Kouvelis VN. Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts. Genome Biol Evol 2022; 14:6586520. [PMID: 35576568 PMCID: PMC9154068 DOI: 10.1093/gbe/evac073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Saccharomycotina yeasts belong to diverse clades within the kingdom of fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 155 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions’ diversity, genetic code alterations, and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process, mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout the evolution of Saccharomycotina. Overall, this work shows that phylogenetic studies based on the mt genome of yeasts highlight major evolutionary events.
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Affiliation(s)
- Anastasia C Christinaki
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Spyros G Kanellopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Alexandra M Kortsinoglou
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Marios Α Andrikopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
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27
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Theelen B, Mixão V, Ianiri G, Goh JPZ, Dijksterhuis J, Heitman J, Dawson TL, Gabaldón T, Boekhout T. Multiple Hybridization Events Punctuate the Evolutionary Trajectory of Malassezia furfur. mBio 2022; 13:e0385321. [PMID: 35404119 PMCID: PMC9040865 DOI: 10.1128/mbio.03853-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 12/18/2022] Open
Abstract
Malassezia species are important fungal skin commensals and are part of the normal microbiota of humans and other animals. However, under certain circumstances these fungi can also display a pathogenic behavior. For example, Malassezia furfur is a common commensal of human skin and yet is often responsible for skin disorders but also systemic infections. Comparative genomics analysis of M. furfur revealed that some isolates have a hybrid origin, similar to several other recently described hybrid fungal pathogens. Because hybrid species exhibit genomic plasticity that can impact phenotypes, we sought to elucidate the genomic evolution and phenotypic characteristics of M. furfur hybrids in comparison to their parental lineages. To this end, we performed a comparative genomics analysis between hybrid strains and their presumptive parental lineages and assessed phenotypic characteristics. Our results provide evidence that at least two distinct hybridization events occurred between the same parental lineages and that the parental strains may have originally been hybrids themselves. Analysis of the mating-type locus reveals that M. furfur has a pseudobipolar mating system and provides evidence that after sexual liaisons of mating compatible cells, hybridization involved cell-cell fusion leading to a diploid/aneuploid state. This study provides new insights into the evolutionary trajectory of M. furfur and contributes with valuable genomic resources for future pathogenicity studies. IMPORTANCEMalassezia furfur is a common commensal member of human/animal microbiota that is also associated with several pathogenic states. Recent studies report involvement of Malassezia species in Crohn's disease, a type of inflammatory bowel disease, pancreatic cancer progression, and exacerbation of cystic fibrosis. A recent genomics analysis of M. furfur revealed the existence of hybrid isolates and identified their putative parental lineages. In this study, we explored the genomic and phenotypic features of these hybrids in comparison to their putative parental lineages. Our results revealed the existence of a pseudobipolar mating system in this species and showed evidence for the occurrence of multiple hybridization events in the evolutionary trajectory of M. furfur. These findings significantly advance our understanding of the evolution of this commensal microbe and are relevant for future studies exploring the role of hybridization in the adaptation to new niches or environments, including the emergence of pathogenicity.
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Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine, Barcelona, Spain
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Joleen Pei Zhen Goh
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research, Singapore
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas L. Dawson
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research, Singapore
- Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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28
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van Thiel IAM, Stavrou AA, de Jong A, Theelen B, Davids M, Hakvoort TBM, Admiraal-van den Berg I, Weert ICM, de Kruijs MAMHV, Vu D, Moissl-Eichinger C, Heinsbroek SEM, Jonkers DMAE, Hagen F, Boekhout T, de Jonge WJ, van den Wijngaard RM. Genetic and phenotypic diversity of fecal Candida albicans strains in irritable bowel syndrome. Sci Rep 2022; 12:5391. [PMID: 35354908 PMCID: PMC8967921 DOI: 10.1038/s41598-022-09436-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/21/2022] [Indexed: 12/16/2022] Open
Abstract
Irritable bowel syndrome (IBS) is a common disorder characterized by chronic abdominal pain and changes in bowel movements. Visceral hypersensitivity is thought to be responsible for pain complaints in a subset of patients. In an IBS-like animal model, visceral hypersensitivity was triggered by intestinal fungi, and lower mycobiota α-diversity in IBS patients was accompanied by a shift toward increased presence of Candida albicans and Saccharomyces cerevisiae. Yet, this shift was observed in hypersensitive as well as normosensitive patients and diversity did not differ between IBS subgroups. The latter suggests that, when a patient changes from hyper- to normosensitivity, the relevance of intestinal fungi is not necessarily reflected in compositional mycobiota changes. We now confirmed this notion by performing ITS1 sequencing on an existing longitudinal set of fecal samples. Since ITS1 methodology does not recognize variations within species, we next focused on heterogeneity within cultured healthy volunteer and IBS-derived C. albicans strains. We observed inter- and intra-individual genomic variation and partial clustering of strains from hypersensitive patients. Phenotyping showed differences related to growth, yeast-to-hyphae morphogenesis and gene expression, specifically of the gene encoding fungal toxin candidalysin. Our investigations emphasize the need for strain-specific cause-and-effect studies within the realm of IBS research.
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Affiliation(s)
- Isabelle A M van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Aimilia A Stavrou
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Auke de Jong
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Mark Davids
- Laboratory of Experimental Vascular Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Theodorus B M Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Iris Admiraal-van den Berg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Isabelle C M Weert
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Martine A M Hesselink-van de Kruijs
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Center for Microbiome Research, Medical University Graz, Graz, Austria
| | - Sigrid E M Heinsbroek
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.,Gastroenterology and Hepatology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Daisy M A E Jonkers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.,Gastroenterology and Hepatology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands. .,Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands. .,Gastroenterology and Hepatology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.
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29
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Semumu T, Gamero A, Boekhout T, Zhou N. Evolutionary engineering to improve Wickerhamomyces subpelliculosus and Kazachstania gamospora for baking. World J Microbiol Biotechnol 2022; 38:48. [PMID: 35089427 DOI: 10.1007/s11274-021-03226-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/30/2021] [Indexed: 10/19/2022]
Abstract
The conventional baker's yeast, Saccharomyces cerevisiae, is the indispensable baking yeast of all times. Its monopoly coupled to its major drawbacks, such as streamlined carbon substrate utilisation base and a poor ability to withstand a number of baking associated stresses, prompt the need to search for alternative yeasts to leaven bread in the era of increasingly complex consumer lifestyles. Our previous work identified the inefficient baking attributes of Wickerhamomyces subpelliculosus and Kazachstania gamospora as well as preliminarily observations of improving the fermentative capacity of these potential alternative baker's yeasts using evolutionary engineering. Here we report on the characterisation and improvement in baking traits in five out of six independently evolved lines incubated for longer time and passaged for at least 60 passages relative to their parental strains as well as the conventional baker's yeast. In addition, the evolved clones produced bread with a higher loaf volume when compared to bread baked with either the ancestral strain or the control conventional baker's yeast. Remarkably, our approach improved the yeasts' ability to withstand baking associated stresses, a key baking trait exhibited poorly in both the conventional baker's yeast and their ancestral strains. W. subpelliculosus evolved the best characteristics attractive for alternative baker's yeasts as compared to the evolved K. gamospora strains. These results demonstrate the robustness of evolutionary engineering in development of alternative baker's yeasts.
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Affiliation(s)
- Thandiwe Semumu
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana.
| | - Amparo Gamero
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, Avda. Vicent Andrés Estellés S/N, Burjassot, 46100, València, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana.
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30
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Salah H, Kolecka A, Rozaliyani A, Wahyuningsih R, Taj-Aldeen SJ, Boekhout T, Houbraken J. A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Mycopathologia 2022; 187:39-52. [PMID: 35006478 PMCID: PMC8807449 DOI: 10.1007/s11046-021-00603-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.
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Affiliation(s)
- Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Rozaliyani
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Retno Wahyuningsih
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Department of Parasitology Faculty of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Saad J Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,University of Babylon, Hilla, Iraq
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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31
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Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J, Coelho MA. Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex. eLife 2022; 11:79114. [PMID: 35713948 PMCID: PMC9296135 DOI: 10.7554/elife.79114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
<title>eLife digest</title>. Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population. Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease. With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility. Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile. Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species. This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Terrance Shea
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity InstituteUtrechtNetherlands,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamNetherlands
| | - Betina M Porcel
- Génomique Métabolique, CNRS, University Evry, Université Paris-SaclayEvryFrance
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität BochumBochumGermany
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
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32
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Stavrou A, Hagen F, Boekhout T, Brouwer C. ID-CARD: A clade-specific molecular assay for the detection of 25 Candida spp. causing candidemia based on antifungal susceptibility patterns and in vitro testing of the antifungal activity of a synthetic antimicrobial peptide derived from human lactoferrin (hLF1-11). Access Microbiol 2021. [DOI: 10.1099/acmi.cc2021.po0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fungal infections are a serious health concern affecting over 1.5 million individuals annually. ID-CARD aims to improve diagnostics taking into account phylogeny and antifungal susceptibility patterns of Candida spp. involved in candidemia.Twenty-five Candida spp. were chosen. Based on ribosomal DNA sequences, clade-specific primers/Taqman probes were designed. Different multiplex panels consisting of four clades that exhibited similar antifungal susceptibility profiles were created. To create the groups, we tested fluconazole and anidulafungin with broth microdilution according to EUCAST against 3-5 isolates/species (n=121), which were also used for specificity testing of the molecular assay. Furthermore, we tested the in vitro activity of hLF(1-11) peptide against isolates that exhibited elevated minimum inhibitory concentrations (MICs) for one or both of the drugs. The groups created are : i. Lodderomyces, Kluyveromyces, Metschnikowiaceae Sensitive, Internal control, (all with low MICs) ii. Pichiaceae, Nakaseomyces, Wickerhamomycetaceae, Debaryomyces & Diutina, (all with high MICs to azoles) and iii. Yarrowia, Wickerhamiella & Meyerozyma, Candida auris, Candida haemulonii complex (all with high MICs to both azoles & echinocandins). The primers/probes showed 100% specificity and capacity for multiplexing. In vitro experiments indicated that hLF(1-11) is fungicidal against various Candidaspp. A synergistic effect of antifungal and hLF(1-11) against various Candida species was shown as combinations of the peptide with antifungals were more effective than these alone ID-CARD will contribute to a fast and reliable molecular detection of yeasts involved in candidiasis. AMPs is a novel way to treat Candida spp. exhibiting high MICs to commonly used antifungal drugs.
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Affiliation(s)
| | - Ferry Hagen
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital
- University Medical Center Utrecht, Department of Medical Microbiology
- Westerdijk fungal Biodiversity Institute, Netherlands
| | - Teun Boekhout
- Westerdijk fungal Biodiversity Institute, Netherlands
| | - Carlo Brouwer
- Westerdijk fungal Biodiversity Institute, Netherlands
- CBMR Scientific Nanoscience BV, Netherlands
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33
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Theelen B, Christinaki AC, Dawson TL, Boekhout T, Kouvelis VN. Comparative analysis of Malassezia furfur mitogenomes and the development of a mitochondria-based typing approach. FEMS Yeast Res 2021; 21:6375414. [PMID: 34562093 PMCID: PMC8510979 DOI: 10.1093/femsyr/foab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
Malassezia furfur is a yeast species belonging to Malasseziomycetes, Ustilaginomycotina and Basidiomycota that is found on healthy warm-blooded animal skin, but also involved in various skin disorders like seborrheic dermatitis/dandruff and pityriasis versicolor. Moreover, Malassezia are associated with bloodstream infections, Crohn's disease and pancreatic carcinoma. Recent advances in Malassezia genomics and genetics have focused on the nuclear genome. In this work, we present the M. furfur mitochondrial (mt) genetic heterogenicity with full analysis of 14 novel and six available M. furfur mt genomes. The mitogenome analysis reveals a mt gene content typical for fungi, including identification of variable mt regions suitable for intra-species discrimination. Three of them, namely the trnK–atp6 and cox3–nad3 intergenic regions and intron 2 of the cob gene, were selected for primer design to identify strain differences. Malassezia furfur strains belonging to known genetic variable clusters, based on AFLP and nuclear loci, were assessed for their mt variation using PCR amplification and sequencing. The results suggest that these mt regions are excellent molecular markers for the typing of M. furfur strains and may provide added value to nuclear regions when assessing evolutionary relationships at the intraspecies level.
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Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Anastasia C Christinaki
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Thomas L Dawson
- Agency for Science, Technology, and Research (A∗STAR), Skin Research Institute of Singapore (SRIS), 11 Mandalay Rd, #17-01, Singapore 308232, Singapore.,Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, 280 Calhoun St, Charleston, SC, 29425, USA
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
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34
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Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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35
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Rhimi W, Theelen B, Boekhout T, Aneke CI, Otranto D, Cafarchia C. Conventional therapy and new antifungal drugs against Malassezia infections. Med Mycol 2021; 59:215-234. [PMID: 33099634 DOI: 10.1093/mmy/myaa087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/14/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
Malassezia yeasts are commensal microorganisms occurring on the skin of humans and animals causing dermatological disorders or systemic infections in severely immunocompromised hosts. Despite attempts to control such yeast infections with topical and systemic antifungals, recurrence of clinical signs of skin infections as well as treatment failure in preventing or treating Malassezia furfur fungemia have been reported most likely due to wrong management of these infections (e.g., due to early termination of treatment) or due to the occurrence of resistant phenomena. Standardized methods for in vitro antifungal susceptibility tests of these yeasts are still lacking, thus resulting in variable susceptibility profiles to azoles among Malassezia spp. and a lack of clinical breakpoints. The inherent limitations to the current pharmacological treatments for Malassezia infections both in humans and animals, stimulated the interest of the scientific community to discover new, effective antifungal drugs or substances to treat these infections. In this review, data about the in vivo and in vitro antifungal activity of the most commonly employed drugs (i.e., azoles, polyenes, allylamines, and echinocandins) against Malassezia yeasts, with a focus on human bloodstream infections, are summarized and their clinical implications are discussed. In addition, the usefulness of alternative compounds is discussed.
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Affiliation(s)
- Wafa Rhimi
- Dipartimento di Medicina Veterinaria, Università degli Studi "Aldo Moro", Bari, Italy
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Chioma Inyang Aneke
- Dipartimento di Medicina Veterinaria, Università degli Studi "Aldo Moro", Bari, Italy.,Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi "Aldo Moro", Bari, Italy.,Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi "Aldo Moro", Bari, Italy
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Mixão V, Saus E, Boekhout T, Gabaldón T. Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans. Genetics 2021; 217:5995314. [PMID: 33724404 PMCID: PMC8045679 DOI: 10.1093/genetics/iyaa004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/03/2020] [Indexed: 01/23/2023] Open
Abstract
Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn. C. albicans var. africana) and Candida stellatoidea (syn. C. albicans var. stellatoidea) being considered different species or C. albicans varieties depending on the authors. Moreover, recent genomic analyses have suggested a shared hybrid origin of C. albicans and C. africana, but the potential parental lineages remain unidentified. Although the genomes of C. albicans and C. africana have been extensively studied, the genome of C. stellatoidea has not been sequenced so far. In order to get a better understanding of the evolution of the C. albicans clade, and to assess whether C. stellatoidea could represent one of the unknown C. albicans parental lineages, we sequenced C. stellatoidea type strain (CBS 1905). This genome was compared to that of C. albicans and of the closely related lineage C. africana. Our results show that, similarly to C. africana, C. stellatoidea descends from the same hybrid ancestor as other C. albicans strains and that it has undergone a parallel massive loss of heterozygosity.
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Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Hafez A, Futami R, Arastehfar A, Daneshnia F, Miguel A, Roig FJ, Soriano B, Perez-Sánchez J, Boekhout T, Gabaldón T, Llorens C. SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. Bioinformatics 2021; 37:1610-1612. [PMID: 33079985 DOI: 10.1093/bioinformatics/btaa903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/07/2020] [Accepted: 10/07/2020] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis. RESULT SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets. AVAILABILITYAND IMPLEMENTATION SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ahmed Hafez
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Faculty of Computers and Information, Minia University, Minia, Egypt
| | - Ricardo Futami
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | - Amir Arastehfar
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Farnaz Daneshnia
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana Miguel
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | - Francisco J Roig
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain.,Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
| | - Beatriz Soriano
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | | | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Toni Gabaldón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carlos Llorens
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
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Yurkov A, Alves A, Bai FY, Boundy-Mills K, Buzzini P, Čadež N, Cardinali G, Casaregola S, Chaturvedi V, Collin V, Fell JW, Girard V, Groenewald M, Hagen F, Hittinger CT, Kachalkin AV, Kostrzewa M, Kouvelis V, Libkind D, Liu X, Maier T, Meyer W, Péter G, Piątek M, Robert V, Rosa CA, Sampaio JP, Sipiczki M, Stadler M, Sugita T, Sugiyama J, Takagi H, Takashima M, Turchetti B, Wang QM, Boekhout T. Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes. IMA Fungus 2021; 12:18. [PMID: 34256869 PMCID: PMC8278710 DOI: 10.1186/s43008-021-00067-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/18/2021] [Indexed: 01/25/2023] Open
Abstract
The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.
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Affiliation(s)
- Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Artur Alves
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, Phaff Yeast Culture Collection, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Neža Čadež
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ul. 101, 1000, Ljubljana, Slovenia
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Valérie Collin
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France
| | - Jack W Fell
- Emeritus Professor, Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, FL, 33149, USA
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - Aleksey V Kachalkin
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1-12, 119991, Moscow, Russia.,All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM RAS), Russian Academy of Sciences, Prospect Nauki 5, 142290, Puschino, Russia
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Vassili Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701, Athens, Greece
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) CONICET - Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Rio Negro, Argentina
| | - Xinzhan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China
| | - Thomas Maier
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, 2006, Australia.,Westmead Institute for Medical Research, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia.,Westmead Hospital (Research and Education Network), Darcy Rd, Westmead, NSW, 2145, Australia
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, Budapest, H-1118, Hungary
| | - Marcin Piątek
- Department of Mycology, W. Szafer Institute of Botany of the Polish Academy of Sciences, Lubicz ul. 46, 31-512, Kraków, Poland
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Carlos A Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Jose Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal.,Departamento de Ciências da Vida, PYCC - Portuguese Yeast Culture Collection, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4010, Hungary
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2 Chome-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Junta Sugiyama
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.,TechnoSuruga Laboratory Co., Ltd., 388-1, Nagasaki, Shimuzu, Shizuoka, 424-0065, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China.,College of Life Sciences, Hebei University, 180 Wusi Dong Road, Lian Chi District, Baoding City, Hebei Province, 071002, People's Republic of China
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, The Netherlands
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Toplis B, Bosch C, Schwartz IS, Kenyon C, Boekhout T, Perfect JR, Botha A. The virulence factor urease and its unexplored role in the metabolism of Cryptococcus neoformans. FEMS Yeast Res 2021; 20:5850754. [PMID: 32490521 DOI: 10.1093/femsyr/foaa031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cryptococcal urease is believed to be important for the degradation of exogenous urea that the yeast encounters both in its natural environment and within the human host. Endogenous urea produced by the yeast's own metabolic reactions, however, may also serve as a substrate for the urease enzyme. Using wild-type, urease-deletion mutant and urease-reconstituted strains of Cryptococcus neoformans H99, we studied reactions located up- and downstream from endogenous urea. We demonstrated that urease is important for cryptococcal growth and that, compared to nutrient-rich conditions at 26°C, urease activity is higher under nutrient-limited conditions at 37°C. Compared to cells with a functional urease enzyme, urease-deficient cells had significantly higher intracellular urea levels and also showed more arginase activity, which may act as a potential source of endogenous urea. Metabolic reactions linked to arginase were also affected, since urease-positive and urease-negative cells differed with respect to agmatinase activity, polyamine synthesis, and intracellular levels of proline and reactive oxygen species. Lastly, urease-deficient cells showed higher melanin levels at 26°C than wild-type cells, while the inverse was observed at 37°C. These results suggest that cryptococcal urease is associated with the functioning of key metabolic pathways within the yeast cell.
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Affiliation(s)
- Barbra Toplis
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| | - Caylin Bosch
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Chris Kenyon
- Sexually Transmitted Infection Unit, Institute of Tropical Medicine, 2000 Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - John R Perfect
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710-1000, North Carolina, USA
| | - Alfred Botha
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
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Arastehfar A, Daneshnia F, Hilmioglu-Polat S, Ilkit M, Yasar M, Polat F, Metin DY, Dokumcu ÜZ, Pan W, Hagen F, Boekhout T, Perlin DS, Lass-Flörl C. Genetically related micafungin-resistant Candida parapsilosis blood isolates harbouring novel mutation R658G in hotspot 1 of Fks1p: a new challenge? J Antimicrob Chemother 2021; 76:418-422. [PMID: 33175162 DOI: 10.1093/jac/dkaa419] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Echinocandin resistance rarely occurs in clinical Candida parapsilosis isolates and the underlying mechanism is unknown. OBJECTIVES To determine the prevalence of echinocandin resistance and the underlying mechanism for a large collection of C. parapsilosis blood isolates and to determine whether the echinocandin-resistant isolates were clonally related. METHODS C. parapsilosis blood isolates (n = 213) were subjected to antifungal susceptibility testing (CLSI M27), for micafungin, anidulafungin, amphotericin B and, if appropriate, caspofungin. Hotspot (HS) 1 and HS2 of FKS1 were sequenced for all isolates (n = 213) and microsatellite typing was performed for echinocandin-resistant isolates. RESULTS All isolates were susceptible to amphotericin B and two isolates were intermediate to anidulafungin (MIC = 4 mg/L), while micafungin resistance was noted in four isolates (MIC >8 mg/L); three of which were also fluconazole resistant and therefore were MDR. Interestingly, micafungin-resistant isolates, but not those intermediate to anidulafungin, carried novel mutation R658G in HS1 of Fks1p; three of which also harboured Y132F+K143R in Erg11. The first isolate (MICR1) was recovered in November 2017 from a patient admitted to paediatric gastroenterology who showed therapeutic failure under caspofungin treatment. MICR2-MICR4 were collected during 2018-19 and were recovered from three echinocandin-naive paediatric-surgery patients; the isolates shared the same genotype. CONCLUSIONS Herein, for the first time (to the best of our knowledge), we identified micafungin-resistant C. parapsilosis blood isolates harbouring a novel mutation in HS1 of FKS1, which was likely attributable to in vitro micafungin resistance and in vivo caspofungin therapeutic failure. The acquisition of micafungin-resistant C. parapsilosis isolates in echinocandin-naive patients likely implicates clonal expansion, as supported by the close genetic relatedness of MICR2-MICR4.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Macit Ilkit
- Divison of Mycology, University of Çukurova, Adana, Turkey
| | - Melike Yasar
- Division of Mycology, University of Ege, Izmir, Turkey
| | - Furkan Polat
- Division of Mycology, University of Ege, Izmir, Turkey
| | | | - Ülküm Zafer Dokumcu
- Department of Paediatric Surgery, Faculty of Medicine, University of Ege, Izmir, Turkey
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Paediatric Surgery, Faculty of Medicine, University of Ege, Izmir, Turkey.,Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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Arastehfar A, de Almeida Júnior JN, Perlin DS, Ilkit M, Boekhout T, Colombo AL. Multidrug-resistant Trichosporon species: underestimated fungal pathogens posing imminent threats in clinical settings. Crit Rev Microbiol 2021; 47:679-698. [PMID: 34115962 DOI: 10.1080/1040841x.2021.1921695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Species of Trichosporon and related genera are widely used in biotechnology and, hence, many species have their genome sequenced. Importantly, yeasts of the genus Trichosporon have been increasingly identified as a cause of life-threatening invasive trichosporonosis (IT) in humans and are associated with an exceptionally high mortality rate. Trichosporon spp. are intrinsically resistant to frontline antifungal agents, which accounts for numerous reports of therapeutic failure when echinocandins are used to treat IT. Moreover, these fungi have low sensitivity to polyenes and azoles and, therefore, are potentially regarded as multidrug-resistant pathogens. However, despite the clinical importance of Trichosporon spp., our understanding of their antifungal resistance mechanisms is quite limited. Furthermore, antifungal susceptibility testing is not standardized, and there is a lack of interpretive epidemiological cut-off values for minimal inhibitory concentrations to distinguish non-wild type Trichosporon isolates. The route of infection remains obscure and detailed clinical and environmental studies are required to determine whether the Trichosporon infections are endogenous or exogenous in nature. Although our knowledge on effective IT treatments is rather limited and future randomized clinical trials are required to identify the best antifungal agent, the current paradigm advocates the use of voriconazole, removal of central venous catheters and recovery from neutropenia.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - João N de Almeida Júnior
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Macit Ilkit
- Division of Mycology, University of Çukurova, Adana, Turkey
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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43
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Arastehfar A, Daneshnia F, Hafez A, Khodavaisy S, Najafzadeh MJ, Charsizadeh A, Zarrinfar H, Salehi M, Shahrabadi ZZ, Sasani E, Zomorodian K, Pan W, Hagen F, Ilkit M, Kostrzewa M, Boekhout T. Antifungal susceptibility, genotyping, resistance mechanism, and clinical profile of Candida tropicalis blood isolates. Med Mycol 2021; 58:766-773. [PMID: 31828316 PMCID: PMC7398758 DOI: 10.1093/mmy/myz124] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Candida tropicalis is one of the major candidaemia agents, associated with the highest mortality rates among Candida species, and developing resistance to azoles. Little is known about the molecular mechanisms of azole resistance, genotypic diversity, and the clinical background of C. tropicalis infections. Consequently, this study was designed to address those questions. Sixty-four C. tropicalis bloodstream isolates from 62 patients from three cities in Iran (2014–2019) were analyzed. Strain identification, antifungal susceptibility testing, and genotypic diversity analysis were performed by MALDI-TOF MS, CLSI-M27 A3/S4 protocol, and amplified fragment length polymorphism (AFLP) fingerprinting, respectively. Genes related to drug resistance (ERG11, MRR1, TAC1, UPC2, and FKS1 hotspot9s) were sequenced. The overall mortality rate was 59.6% (37/62). Strains were resistant to micafungin [minimum inhibitory concentration (MIC) ≥1 μg/ml, 2/64], itraconazole (MIC > 0.5 μg/ml, 2/64), fluconazole (FLZ; MIC ≥ 8 μg/ml, 4/64), and voriconazole (MIC ≥ 1 μg/ml, 7/64). Pan-azole and FLZ + VRZ resistance were observed in one and two isolates, respectively, while none of the patients were exposed to azoles. MRR1 (T255P, 647S), TAC1 (N164I, R47Q), and UPC2 (T241A, Q340H, T381S) mutations were exclusively identified in FLZ-resistant isolates. AFLP fingerprinting revealed five major and seven minor genotypes; genotype G4 was predominant in all centers. The increasing number of FLZ-R C. tropicalis blood isolates and acquiring FLZ-R in FLZ-naive patients limit the efficiency of FLZ, especially in developing countries. The high mortality rate warrants reaching a consensus regarding the nosocomial mode of C. tropicalis transmission.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arezoo Charsizadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Salehi
- Department of infectious diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Zare Shahrabadi
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Sasani
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Weihua Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | | | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam1012 WX, The Netherlands
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44
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Rhimi W, Aneke CI, Annoscia G, Otranto D, Boekhout T, Cafarchia C. Effect of chlorogenic and gallic acids combined with azoles on antifungal susceptibility and virulence of multidrug-resistant Candida spp. and Malassezia furfur isolates. Med Mycol 2021; 58:1091-1101. [PMID: 32236482 DOI: 10.1093/mmy/myaa010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/03/2023] Open
Abstract
Chlorogenic acid (CHA) and gallic acid (GA) are safe natural phenolic compounds that are used as enhancers of some drugs in influencing antioxidant, anticancer, and antibacterial activities. Among fungi, Candida spp. and Malassezia spp. are characterized by an increasing prevalence of multidrug resistance phenomena and by a high morbidity and mortality of their infections. No data are available about the efficacy of CHA and GA combined with azoles on the antifungal susceptibility and on the virulence of both fungi. Therefore, their antifungal and antivirulence effects have been tested in combination with fluconazole (FLZ) or ketoconazole (KTZ) on 23 Candida spp. and 8 M. furfur isolates. Broth microdilution chequerboard, time-kill studies, and extracellular enzymes (phospholipase and hemolytic) activities were evaluated, displaying a synergistic antifungal action between CHA or GA and FLZ or KTZ on C. albicans, C. bovina, and C. parapsilosis, and antagonistic antifungal effects on M. furfur and Pichia kudriavzevii (Candida krusei) isolates. The time-kill studies confirmed the chequerboard findings, showing fungicidal inhibitory effect only when the GA was combined with azoles on Candida strains. However, the combination of phenolics with azoles had no effect on the virulence of the tested isolates. Our study indicates that the combination between natural products and conventional drugs could be an efficient strategy for combating azole resistance and for controlling fungistatic effects of azole drugs.
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Affiliation(s)
- Wafa Rhimi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Aldo Moro, Bari, Italy
| | - Chioma Inyang Aneke
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Aldo Moro, Bari, Italy.,Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Giada Annoscia
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Aldo Moro, Bari, Italy
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Aldo Moro, Bari, Italy
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,The Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Aldo Moro, Bari, Italy
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45
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Nwaefuna AE, Rumbold K, Boekhout T, Zhou N. Bioethanolic yeasts from dung beetles: tapping the potential of extremophilic yeasts for improvement of lignocellulolytic feedstock fermentation. Biotechnol Biofuels 2021; 14:86. [PMID: 33827664 PMCID: PMC8028181 DOI: 10.1186/s13068-021-01940-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 03/27/2021] [Indexed: 05/10/2023]
Abstract
Bioethanol from abundant and inexpensive agricultural and industrial wastes possesses the potential to reduce greenhouse gas emissions. Bioethanol as renewable fuel addresses elevated production costs, as well as food security concerns. Although technical advancements in simultaneous saccharification and fermentation have reduced the cost of production, one major drawback of this technology is that the pre-treatment process creates environmental stressors inhibitory to fermentative yeasts subsequently reducing bioethanol productivity. Robust fermentative yeasts with extreme stress tolerance remain limited. This review presents the potential of dung beetles from pristine and unexplored environments as an attractive source of extremophilic bioethanolic yeasts. Dung beetles survive on a recalcitrant lignocellulose-rich diet suggesting the presence of symbiotic yeasts with a cellulolytic potential. Dung beetles inhabiting extreme stress environments have the potential to harbour yeasts with the ability to withstand inhibitory environmental stresses typically associated with bioethanol production. The review further discusses established methods used to isolate bioethanolic yeasts, from dung beetles.
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Affiliation(s)
- Anita Ejiro Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
| | - Karl Rumbold
- Industrial Microbiology and Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, the Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1098 SM Amsterdam, the Netherlands
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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46
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Crous P, Lombard L, Sandoval-Denis M, Seifert K, Schroers HJ, Chaverri P, Gené J, Guarro J, Hirooka Y, Bensch K, Kema G, Lamprecht S, Cai L, Rossman A, Stadler M, Summerbell R, Taylor J, Ploch S, Visagie C, Yilmaz N, Frisvad J, Abdel-Azeem A, Abdollahzadeh J, Abdolrasouli A, Akulov A, Alberts J, Araújo J, Ariyawansa H, Bakhshi M, Bendiksby M, Ben Hadj Amor A, Bezerra J, Boekhout T, Câmara M, Carbia M, Cardinali G, Castañeda-Ruiz R, Celis A, Chaturvedi V, Collemare J, Croll D, Damm U, Decock C, de Vries R, Ezekiel C, Fan X, Fernández N, Gaya E, González C, Gramaje D, Groenewald J, Grube M, Guevara-Suarez M, Gupta V, Guarnaccia V, Haddaji A, Hagen F, Haelewaters D, Hansen K, Hashimoto A, Hernández-Restrepo M, Houbraken J, Hubka V, Hyde K, Iturriaga T, Jeewon R, Johnston P, Jurjević Ž, Karalti İ, Korsten L, Kuramae E, Kušan I, Labuda R, Lawrence D, Lee H, Lechat C, Li H, Litovka Y, Maharachchikumbura S, Marin-Felix Y, Matio Kemkuignou B, Matočec N, McTaggart A, Mlčoch P, Mugnai L, Nakashima C, Nilsson R, Noumeur S, Pavlov I, Peralta M, Phillips A, Pitt J, Polizzi G, Quaedvlieg W, Rajeshkumar K, Restrepo S, Rhaiem A, Robert J, Robert V, Rodrigues A, Salgado-Salazar C, Samson R, Santos A, Shivas R, Souza-Motta C, Sun G, Swart W, Szoke S, Tan Y, Taylor J, Taylor P, Tiago P, Váczy K, van de Wiele N, van der Merwe N, Verkley G, Vieira W, Vizzini A, Weir B, Wijayawardene N, Xia J, Yáñez-Morales M, Yurkov A, Zamora J, Zare R, Zhang C, Thines M. Fusarium: more than a node or a foot-shaped basal cell. Stud Mycol 2021; 98:100116. [PMID: 34466168 PMCID: PMC8379525 DOI: 10.1016/j.simyco.2021.100116] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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Key Words
- Apiognomonia platani (Lév.) L. Lombard
- Atractium ciliatum Link
- Atractium pallidum Bonord.
- Calloria tremelloides (Grev.) L. Lombard
- Cephalosporium sacchari E.J. Butler
- Cosmosporella cavisperma (Corda) Sand.-Den., L. Lombard & Crous
- Cylindrodendrum orthosporum (Sacc. & P. Syd.) L. Lombard
- Dialonectria volutella (Ellis & Everh.) L. Lombard & Sand.-Den.
- Fusarium aeruginosum Delacr.
- Fusarium agaricorum Sarrazin
- Fusarium albidoviolaceum Dasz.
- Fusarium aleyrodis Petch
- Fusarium amentorum Lacroix
- Fusarium annuum Leonian
- Fusarium arcuatum Berk. & M.A. Curtis
- Fusarium aridum O.A. Pratt
- Fusarium armeniacum (G.A. Forbes et al.) L.W. Burgess & Summerell
- Fusarium arthrosporioides Sherb.
- Fusarium asparagi Delacr.
- Fusarium batatas Wollenw.
- Fusarium biforme Sherb.
- Fusarium buharicum Jacz. ex Babajan & Teterevn.-Babajan
- Fusarium cactacearum Pasin. & Buzz.-Trav.
- Fusarium cacti-maxonii Pasin. & Buzz.-Trav.
- Fusarium caudatum Wollenw.
- Fusarium cavispermum Corda
- Fusarium cepae Hanzawa
- Fusarium cesatii Rabenh.
- Fusarium citriforme Jamal.
- Fusarium citrinum Wollenw.
- Fusarium citrulli Taubenh.
- Fusarium clavatum Sherb.
- Fusarium coccinellum Kalchbr.
- Fusarium cromyophthoron Sideris
- Fusarium cucurbitae Taubenh.
- Fusarium cuneiforme Sherb.
- Fusarium delacroixii Sacc.
- Fusarium dimerum var. nectrioides Wollenw.
- Fusarium echinatum Sand.-Den. & G.J. Marais
- Fusarium epicoccum McAlpine
- Fusarium eucheliae Sartory, R. Sartory & J. Mey.
- Fusarium fissum Peyl
- Fusarium flocciferum Corda
- Fusarium gemmiperda Aderh.
- Fusarium genevense Dasz.
- Fusarium graminearum Schwabe
- Fusarium graminum Corda
- Fusarium heterosporioides Fautrey
- Fusarium heterosporum Nees & T. Nees
- Fusarium idahoanum O.A. Pratt
- Fusarium juruanum Henn.
- Fusarium lanceolatum O.A. Pratt
- Fusarium lateritium Nees
- Fusarium loncheceras Sideris
- Fusarium longipes Wollenw. & Reinking
- Fusarium lyarnte J.L. Walsh, Sangal., L.W. Burgess, E.C.Y. Liew & Summerell
- Fusarium malvacearum Taubenh.
- Fusarium martii f. phaseoli Burkh.
- Fusarium muentzii Delacr.
- Fusarium nigrum O.A. Pratt
- Fusarium oxysporum var. asclerotium Sherb.
- Fusarium palczewskii Jacz.
- Fusarium palustre W.H. Elmer & Marra
- Fusarium polymorphum Matr.
- Fusarium poolense Taubenh.
- Fusarium prieskaense G.J. Marais & Sand.-Den.
- Fusarium prunorum McAlpine
- Fusarium pusillum Wollenw.
- Fusarium putrefaciens Osterw.
- Fusarium redolens Wollenw.
- Fusarium reticulatum Mont.
- Fusarium rhizochromatistes Sideris
- Fusarium rhizophilum Corda
- Fusarium rhodellum McAlpine
- Fusarium roesleri Thüm.
- Fusarium rostratum Appel & Wollenw.
- Fusarium rubiginosum Appel & Wollenw.
- Fusarium rubrum Parav.
- Fusarium samoense Gehrm.
- Fusarium scirpi Lambotte & Fautrey
- Fusarium secalis Jacz.
- Fusarium spinaciae Hungerf.
- Fusarium sporotrichioides Sherb.
- Fusarium stercoris Fuckel
- Fusarium stilboides Wollenw.
- Fusarium stillatum De Not. ex Sacc.
- Fusarium sublunatum Reinking
- Fusarium succisae Schröt. ex Sacc.
- Fusarium tabacivorum Delacr.
- Fusarium trichothecioides Wollenw.
- Fusarium tritici Liebman
- Fusarium tuberivorum Wilcox & G.K. Link
- Fusarium tumidum var. humi Reinking
- Fusarium ustilaginis Kellerm. & Swingle
- Fusarium viticola Thüm.
- Fusarium werrikimbe J.L. Walsh, L.W. Burgess, E.C.Y. Liew & B.A. Summerell
- Fusarium willkommii Lindau
- Fusarium xylarioides Steyaert
- Fusarium zygopetali Delacr.
- Fusicolla meniscoidea L. Lombard & Sand.-Den.
- Fusicolla quarantenae J.D.P. Bezerra, Sand.-Den., Crous & Souza-Motta
- Fusicolla sporellula Sand.-Den. & L. Lombard
- Fusisporium andropogonis Cooke ex Thüm.
- Fusisporium anthophilum A. Braun
- Fusisporium arundinis Corda
- Fusisporium avenaceum Fr.
- Fusisporium clypeaster Corda
- Fusisporium culmorum Wm.G. Sm.
- Fusisporium didymum Harting
- Fusisporium elasticae Thüm.
- Fusisporium episphaericum Cooke & Ellis
- Fusisporium flavidum Bonord.
- Fusisporium hordei Wm.G. Sm.
- Fusisporium incarnatum Roberge ex Desm.
- Fusisporium lolii Wm.G. Sm.
- Fusisporium pandani Corda
- Gibberella phyllostachydicola W. Yamam.
- Hymenella aurea (Corda) L. Lombard
- Hymenella spermogoniopsis (Jul. Müll.) L. Lombard & Sand.-Den.
- Luteonectria Sand.-Den., L. Lombard, Schroers & Rossman
- Luteonectria albida (Rossman) Sand.-Den. & L. Lombard
- Luteonectria nematophila (Nirenberg & Hagedorn) Sand.-Den. & L. Lombard
- Macroconia bulbipes Crous & Sand.-Den.
- Macroconia phlogioides Sand.-Den. & Crous
- Menispora penicillata Harz
- Multi-gene phylogeny
- Mycotoxins
- Nectriaceae
- Neocosmospora
- Neocosmospora epipeda Quaedvl. & Sand.-Den.
- Neocosmospora floridana (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora merkxiana Quaedvl. & Sand.-Den.
- Neocosmospora neerlandica Crous & Sand.-Den.
- Neocosmospora nelsonii Crous & Sand.-Den.
- Neocosmospora obliquiseptata (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora pseudopisi Sand.-Den. & L. Lombard
- Neocosmospora rekana (Lynn & Marinc.) L. Lombard & Sand.-Den.
- Neocosmospora tuaranensis (T. Aoki et al.) L. Lombard & Sand.-Den.
- Nothofusarium Crous, Sand.-Den. & L. Lombard
- Nothofusarium devonianum L. Lombard, Crous & Sand.-Den.
- Novel taxa
- Pathogen
- Scolecofusarium L. Lombard, Sand.-Den. & Crous
- Scolecofusarium ciliatum (Link) L. Lombard, Sand.-Den. & Crous
- Selenosporium equiseti Corda
- Selenosporium hippocastani Corda
- Selenosporium sarcochroum Desm
- Selenosporium urticearum Corda.
- Setofusarium (Nirenberg & Samuels) Crous & Sand.-Den.
- Setofusarium setosum (Samuels & Nirenberg) Sand.-Den. & Crous.
- Sphaeria sanguinea var. cicatricum Berk.
- Sporotrichum poae Peck.
- Stylonectria corniculata Gräfenhan, Crous & Sand.-Den.
- Stylonectria hetmanica Akulov, Crous & Sand.-Den.
- Taxonomy
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Affiliation(s)
- P.W. Crous
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - K.A. Seifert
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - H.-J. Schroers
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000, Ljubljana, Slovenia
| | - P. Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - J. Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - Y. Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, 184-8584, Japan
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - G.H.J. Kema
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - A.Y. Rossman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, 97330, USA
| | - M. Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - J.W. Taylor
- Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA, 94720-3102, USA
| | - S. Ploch
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - A.M. Abdel-Azeem
- Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - J. Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - A. Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - A. Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022, Kharkiv, Ukraine
| | - J.F. Alberts
- Department of Food Science and Technology, Cape Peninsula University of Technology, P.O. Box 1906, Bellville, 7535, South Africa
| | - J.P.M. Araújo
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - H.A. Ariyawansa
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 106, Taiwan, ROC
| | - M. Bakhshi
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - M. Bendiksby
- Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - A. Ben Hadj Amor
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - J.D.P. Bezerra
- Setor de Micologia/Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n – Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás/Federal University of Goiás, Goiânia, Brazil
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M.P.S. Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - M. Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina – Universidad de la República, Av. A. Navarro 3051, Montevideo, Uruguay
| | - G. Cardinali
- Department of Pharmaceutical Science, University of Perugia, Via Borgo 20 Giugno, 74 Perugia, Italy
| | - R.F. Castañeda-Ruiz
- Instituto de Investigaciones Fundamentales en Agricultura Tropical Alejandro de Humboldt (INIFAT), Académico Titular de la Academia de Ciencias de, Cuba
| | - A. Celis
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, 111711, Colombia
| | - V. Chaturvedi
- Mycology Laboratory, New York State Department of Health Wadsworth Center, Albany, NY, USA
| | - J. Collemare
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, CH-2000, Neuchatel, Switzerland
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806, Görlitz, Germany
| | - C.A. Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute – ELIM – Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348, Louvain-la-Neuve, Belgium
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - X.L. Fan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - N.B. Fernández
- Laboratorio de Micología Clínica, Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - E. Gaya
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - C.D. González
- Laboratorio de Salud de Bosques y Ecosistemas, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, casilla 567, Valdivia, Chile
| | - D. Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño, 26007, Spain
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Grube
- Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010, Graz, Austria
| | - M. Guevara-Suarez
- Applied genomics research group, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - V.K. Gupta
- Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - V. Guarnaccia
- Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095, Grugliasco, TO, Italy
| | | | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, 35 K.L. Ledeganckstraat, 9000, Ghent, Belgium
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - K. Hansen
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - A. Hashimoto
- Microbe Division/Japan Collection of Microorganisms RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K.D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chaing Rai, 57100, Thailand
| | - T. Iturriaga
- Cornell University, 334 Plant Science Building, Ithaca, NY, 14850, USA
| | - R. Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - P.R. Johnston
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Ž. Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ, 08077, USA
| | - İ. Karalti
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Yeditepe University, Turkey
| | - L. Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria, 0002, South Africa
| | - E.E. Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - I. Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - R. Labuda
- University of Veterinary Medicine, Vienna (VetMed), Institute of Food Safety, Food Technology and Veterinary Public Health, Veterinaerplatz 1, 1210 Vienna and BiMM – Bioactive Microbial Metabolites group, 3430 Tulln a.d. Donau, Austria
| | - D.P. Lawrence
- University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - H.B. Lee
- Department of Agricultural Biological Chemistry, College of Agriculture & Life Sciences, Chonnam National University, Yongbong-Dong 300, Buk-Gu, Gwangju, 61186, South Korea
| | - C. Lechat
- Ascofrance, 64 route de Chizé, 79360, Villiers-en-Bois, France
| | - H.Y. Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Y.A. Litovka
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - S.S.N. Maharachchikumbura
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Y. Marin-Felix
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - B. Matio Kemkuignou
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - N. Matočec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - A.R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, G.P.O. Box 267, Brisbane, 4001, Australia
| | - P. Mlčoch
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - L. Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology section, University of Florence, P.le delle Cascine 28, 50144, Firenze, Italy
| | - C. Nakashima
- Graduate school of Bioresources, Mie University, Kurima-machiya 1577, Tsu, Mie, 514-8507, Japan
| | - R.H. Nilsson
- Gothenburg Global Biodiversity Center at the Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | - S.R. Noumeur
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences, University of Batna 2, Batna, 05000, Algeria
| | - I.N. Pavlov
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - M.P. Peralta
- Laboratorio de Micodiversidad y Micoprospección, PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Argentina
| | - A.J.L. Phillips
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Campo Grande, 1749-016, Lisbon, Portugal
| | - J.I. Pitt
- Microbial Screening Technologies, 28 Percival Rd, Smithfield, NSW, 2164, Australia
| | - G. Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - W. Quaedvlieg
- Phytopathology, Van Zanten Breeding B.V., Lavendelweg 15, 1435 EW, Rijsenhout, the Netherlands
| | - K.C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra, 411 004, India
| | - S. Restrepo
- Laboratory of Mycology and Phytopathology – (LAMFU), Department of Chemical and Food Engineering, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - A. Rhaiem
- Plant Pathology and Population Genetics, Laboratory of Microorganisms, National Gene Bank, Tunisia
| | | | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - C. Salgado-Salazar
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.C.S. Santos
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - R.G. Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
| | - C.M. Souza-Motta
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - G.Y. Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - W.J. Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | | | - Y.P. Tan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland, 4102, Australia
| | - J.E. Taylor
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom
| | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - P.V. Tiago
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - K.Z. Váczy
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300, Eger, Hungary
| | | | - N.A. van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - W.A.S. Vieira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125, Torino, Italy
| | - B.S. Weir
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - N.N. Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - J.W. Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - M.J. Yáñez-Morales
- Fitosanidad, Colegio de Postgraduados-Campus Montecillo, Montecillo-Texcoco, 56230 Edo. de Mexico, Mexico
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36, Uppsala, Sweden
| | - R. Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - C.L. Zhang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
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Wang MM, Groenewald M, Wu F, Guo YT, Wang QM, Boekhout T. Intraspecific nucleotide divergence in Saccharomycodes ludwigii, and proposal of Saccharomycodes pseudoludwigii sp. nov, a new apiculate yeast isolated from China. Antonie Van Leeuwenhoek 2021; 114:553-559. [PMID: 33624171 DOI: 10.1007/s10482-021-01540-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/10/2021] [Indexed: 11/25/2022]
Abstract
The six synonyms currently accepted under Saccharomycodes ludwigii were investigated for by phenotypic properties, however, the sequence diversity of the rRNA and protein coding genes have not yet been determined. Nine strains including the type strains of synonyms of S. ludwigii deposited in the CBS yeast collection, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands, were analyzed using a multi-locus sequence analysis (MLSA) approach that included sequences of 18S ribosomal RNA (rRNA), the D1/D2 domains of the 26S rRNA, the ITS region (including the 5.8S rRNA) and fragments of genes encoding the largest subunit of the RNA polymerase II (RPB1 and RPB2) and translation elongation factor 1-α (TEF1). Our results showed that the nine strains have identical D1/D2, 18S and RPB2 sequences and similar ITS, RPB1 and TEF1 sequences, which indicated that they are conspecific. In addition, a novel species of Saccharomycodes, S. pseudoludwigii sp. nov. (type CGMCC 2.4526 T) that was isolated from fruit and tree bark in China, is proposed. The MycoBank number of this new species is MB 811,650.
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Affiliation(s)
- Man-Man Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Feng Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yun-Tong Guo
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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Arastehfar A, Khanjari S, Zareshahrabadi Z, Fang W, Pan W, Asadpour E, Daneshnia F, Ilkit M, Boekhout T, Perlin DS, Zand F, Zomorodian K. Clinical and microbiological features of candiduria in critically ill adult patients in Shiraz, Iran (2016-2018): deviations from international guidelines and fluconazole therapeutic failure. Med Mycol 2020; 59:myaa092. [PMID: 33305331 DOI: 10.1093/mmy/myaa092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
Candiduria is common among patients admitted to intensive care units (ICUs); however, clinical and microbiological data are limited, which accounts for non-compliance with international guidelines, including over treatment of asymptomatic candiduria that promotes antifungal resistance. This prospective study included adult patients admitted to ICUs of five referral hospitals in Shiraz, Iran, during 2016-2018. Species were identified by MALDI-TOF MS, and antifungal susceptibility was assessed according to CLSI M27-A3/S4. Among 2086 patients, 162 and 293 developed candiduria and bacteriuria, respectively. In total, 174 yeast isolates were collected; 88.5% were Candida albicans (91/174; 52.2%), C. glabrata (38/174; 21.8%), and C. tropicalis (25/174; 14.3%). Antifungal resistance was rare; only two isolates (one C. tropicalis and one C. krusei) were fluconazole resistant. Symptomatic candiduria was noted in 31.4% of patients (51/162); only 37% (19/51) of them were treated and 36.82% (7/19) showed fluconazole therapeutic failure. Two symptomatic patients developed candidemia shortly after candiduria. Among asymptomatic patients, 31.5% (35/111) were overtreated with fluconazole. The mortality rate was 25.3% (41/162); it did not differ between symptomatic and asymptomatic patients. Our results indicate that deviation from standard-of-care treatment for candiduria is a matter of concern given the high rate of fluconazole therapeutic failure among patients with symptomatic candiduria. LAY SUMMARY Candiduria is an underestimated clinical presentation among critically ill patients and detailed data are scarce in this regard. Given the high rate of fluconazole therapeutic failure and development of candidemia in some cases, the mistreatment of candiduria should not be overlooked by clinicians.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Sara Khanjari
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Zareshahrabadi
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Elham Asadpour
- Shiraz Anesthesiology and Critical Care Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Teun Boekhout
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystems Dynamics (IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Farid Zand
- Shiraz Anesthesiology and Critical Care Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Anesthesia and Critical Care Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Vreulink JM, Boekhout T, Vismer H, Botha A. The growth of Cryptococcus gattii MATα and MATa strains is affected by the chemical composition of their woody debris substrate. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Vatanshenassan M, Boekhout T, Mauder N, Robert V, Maier T, Meis JF, Berman J, Then E, Kostrzewa M, Hagen F. Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris. J Fungi (Basel) 2020; 6:jof6030146. [PMID: 32854308 PMCID: PMC7576496 DOI: 10.3390/jof6030146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.
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Affiliation(s)
- Mansoureh Vatanshenassan
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Norman Mauder
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- BioAware, B-4280 Hannut, Belgium
| | - Thomas Maier
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands;
- Center of Expertise in Mycology Radboudumc, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, 80060-000 Curitiba, Brazil
| | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, 6997801 Tel Aviv, Israel;
| | - Euníce Then
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
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