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A new species concept for the clinically relevant Mucor circinelloides complex. Persoonia - Molecular Phylogeny and Evolution of Fungi 2019; 44:67-97. [PMID: 33116336 PMCID: PMC7567969 DOI: 10.3767/persoonia.2020.44.03] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/10/2019] [Indexed: 12/18/2022]
Abstract
Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) and used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently isolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives (Mucor circinelloides complex – MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised taxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of five markers (ITS, rpb1, tsr1, mcm7, and cfs, introduced here) were performed, combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. Five of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of M. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores only indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have been implemented in human infection: M. circinelloides, M. griseocyanus, M. janssenii, M. lusitanicus, M. ramosissimus, M. variicolumellatus, and M. velutinosus.
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Carbon assimilation profiles of mucoralean fungi show their metabolic versatility. Sci Rep 2019; 9:11864. [PMID: 31413281 PMCID: PMC6694110 DOI: 10.1038/s41598-019-48296-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/25/2019] [Indexed: 11/08/2022] Open
Abstract
Most mucoralean fungi are common soil saprotrophs and were probably among the first land colonisers. Although Mucoromycotina representatives grow well on simple sugar media and are thought to be unable to assimilate more complex organic compounds, they are often isolated from plant substrates. The main goal of the study was to explore the effects of isolation origin and phylogenetic placement on the carbon assimilation capacities of a large group of saprotrophic Mucoromycotina representatives (i.e. Umbelopsidales and Mucorales). Fifty two strains representing different Mucoromycotina families and isolated from different substrates were tested for their capacity to grow on 99 different carbon sources using the Biolog phenotypic microarray system and agar plates containing selected biopolymers (i.e. cellulose, xylan, pectin, and starch) as a sole carbon source. Although our results did not reveal a correlation between phylogenetic distance and carbon assimilation capacities, we observed 20 significant differences in growth capacity on specific carbon sources between representatives of different families. Our results also suggest that isolation origin cannot be considered as a main predictor of the carbon assimilation capacities of a particular strain. We conclude that saprotrophic Mucoromycotina representatives are, contrary to common belief, metabolically versatile and able to use a wide variety of carbon sources.
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Sandona K, Billingsley Tobias TL, Hutchinson MI, Natvig DO, Porras-Alfaro A. Diversity of thermophilic and thermotolerant fungi in corn grain. Mycologia 2019; 111:719-729. [PMID: 31348716 DOI: 10.1080/00275514.2019.1631137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Corn bins in the midwestern United States can reach temperatures up to 52 C. High temperatures combined with sufficient moisture and humidity in bins provide the perfect environment to promote the growth of thermophilic and thermotolerant fungi. In this article, we characterize for the first time thermophilic and thermotolerant fungi in corn grain bins using culture-based methods and pyrosequencing techniques. Corn samples were collected from local farms in western Illinois. Samples were plated and incubated at 50 C using a variety of approaches. Of several hundred kernels examined, more than 90% showed colonization. Species identified using culture methods included Thermomyces lanuginosus, Thermomyces dupontii, Aspergillus fumigatus, Thermoascus crustaceus, and Rhizomucor pusillus. Pyrosequencing was also performed directly on corn grain using fungal-specific primers to determine whether thermophilic fungi could be detected using this technique. Sequences were dominated by pathogenic fungi, and thermophiles were represented by less than 2% of the sequences despite being isolated from 90% of the grain samples using culturing techniques. The high abundance of previously undocumented viable fungi in corn could have negative implications for grain quality and pose a potential risk for workers and consumers of corn-derived products in the food industry. Members of the Sordariales were absent among thermophile isolates and were not represented in nuc rDNA internal transcribed spacer (ITS) sequences. This is in striking contrast with results obtained with other substrates such as litter, dung, and soils, where mesophilic and thermophilic members of the Sordariaceae and Chaetomiaceae are common. This absence appears to reflect an important difference between the ecology of Sordariales and other orders within the Ascomycota in terms of their ability to compete in microhabitats rich in sugars and living tissues.
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Affiliation(s)
- Katrina Sandona
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Terri L Billingsley Tobias
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Miriam I Hutchinson
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Donald O Natvig
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Andrea Porras-Alfaro
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455.,Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
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Maleitzke T, Stahnke K, Trampuz A, Märdian S. A case report of cutaneous mucormycosis of the hand after minor trauma in a patient with acute myeloid leukaemia. Trauma Case Rep 2019; 23:100221. [PMID: 31360744 PMCID: PMC6637271 DOI: 10.1016/j.tcr.2019.100221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2019] [Indexed: 11/23/2022] Open
Abstract
Background Mucormycosis is a rare but life-threatening infection, caused by fungi of the Mucorales order, which can be found in soil, rotting leaves or on animals. Through characteristic angioinvasive growth, infections with mucor spores can occur as a pulmonary, rhinocerebral or cutaneous form. Infections mainly affect immunosuppressed patients with a history of uncontrolled diabetes or haematological malignancies, among others. Treatment is multimodal and requires an immediate combination of intravenous amphotericin B therapy and serial surgical debridements. Only a limited number of cases of cutaneous mucormycosis of the hand have been documented and described previously. Case presentation We report a cutaneous mucormycosis in an elderly patient with a therapy-resistant acute myeloid leukaemia after a minor trauma on his right hand, sustained whilst gardening. The fungal infection was treated with serial radical debridements, vacuum-assisted negative-pressure wound closure technique and intravenous antifungals. Despite successful eradication of the fungal infection, a palliative open wound care concept was implemented during the terminal course of the patient's leukaemia. Conclusions Cutaneous mucormycosis is a rare but fulminant fungal infection mostly affecting immunosuppressed patients. Survival is possible when diagnosed and treated early, yet mortality rates remain high.
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Affiliation(s)
- Tazio Maleitzke
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.,Julius Wolff Institute, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.,Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Katharina Stahnke
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Andrej Trampuz
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sven Märdian
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Prakash H, Singh S, Rudramurthy SM, Singh P, Mehta N, Shaw D, Ghosh AK. An aero mycological analysis of Mucormycetes in indoor and outdoor environments of northern India. Med Mycol 2019; 58:118-123. [DOI: 10.1093/mmy/myz031] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/06/2019] [Accepted: 03/15/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mucormycosis is an angio-invasive infection, predominantly acquired by inhalation of sporangiospores from the environment. However, the burden of Mucormycetes sporangiospores in the air is not well studied. We aimed to estimate the burden of Mucormycetes spores in the outdoor and indoor (hospital) environment across different seasons in north India. A total of 380 air samples from outdoor (n = 180) and indoor (n = 200) environment were included in the study. Air samples were suctioned using air sampler (100 l/min) and cultured on Dichloran Rose Bengal Chloramphenicol (DRBC) with benomyl for selective isolation of Mucormycetes. The isolates were identified by phenotypic and genotypic methods. The mean spore count (±SD) of Mucormycetes (cfu/m3) in outdoor samples varied from 0.73 (±0.96) to 8.60 (±5.70) across different seasons. In hospital, the mean spore count varied from 0.68 (±1.07) to 1.12 (±1.07) and 0.88 (±1.01) to 1.72 (±2.17) for air-conditioned wards and non-air-conditioned wards, respectively. Rhizopus arrhizus was the predominant agent isolated from both indoor and outdoor environment followed by Cunninghamella species. We also report a single isolate of the rare mucormycete agent, Apophysomyces variabilis from outdoor environment. The present study highlights the presence of low spore burden of Mucormycetes in outdoor and hospital settings in north India. This study also reports the first isolation of A. variabilis from air samples in the Indian subcontinent.
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Affiliation(s)
- Hariprasath Prakash
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Pankaj Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neha Mehta
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Dipika Shaw
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anup Kumar Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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57
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Hassan MIA, Voigt K. Pathogenicity patterns of mucormycosis: epidemiology, interaction with immune cells and virulence factors. Med Mycol 2019; 57:S245-S256. [PMID: 30816980 PMCID: PMC6394756 DOI: 10.1093/mmy/myz011] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/20/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022] Open
Abstract
Fungi of the basal lineage order Mucorales are able to cause infections in animals and humans. Mucormycosis is a well-known, life-threatening disease especially in patients with a compromised immune system. The rate of mortality and morbidity caused by mucormycosis has increased rapidly during the last decades, especially in developing countries. The systematic, phylogenetic, and epidemiological distributions of mucoralean fungi are addressed in relation to infection in immunocompromised patients. The review highlights the current achievements in (i) diagnostics and management of mucormycosis, (ii) the study of the interaction of Mucorales with cells of the innate immune system, (iii) the assessment of the virulence of Mucorales in vertebrate and invertebrate infection models, and (iv) the determination of virulence factors that are key players in the infection process, for example, high-affinity iron permease (FTR1), spore coat protein (CotH), alkaline Rhizopus protease enzyme (ARP), ADP-ribosylation factor (ARF), dihydrolipoyl dehydrogenase, calcineurin (CaN), serine and aspartate proteases (SAPs). The present mini-review attempts to increase the awareness of these difficult-to-manage fungal infections and to encourage research in the detection of ligands and receptors as potential diagnostic parameters and drug targets.
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Affiliation(s)
- Mohamed I Abdelwahab Hassan
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Adolf-Reichwein-Strasse 23, 07745 Jena, Germany
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Faculty of Biological Sciences, University of Jena, Neugasse 25, 07743 Jena, Germany
- Pests and Plant Protection Department, National Research Centre, 33rd El Buhouth Street (Postal code: 12622) Dokki, Giza, Egypt
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Adolf-Reichwein-Strasse 23, 07745 Jena, Germany
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Faculty of Biological Sciences, University of Jena, Neugasse 25, 07743 Jena, Germany
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58
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Animal Models to Study Mucormycosis. J Fungi (Basel) 2019; 5:jof5020027. [PMID: 30934788 PMCID: PMC6617025 DOI: 10.3390/jof5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Mucormycosis is a rare but often fatal or debilitating infection caused by a diverse group of fungi. Animal models have been crucial in advancing our knowledge of mechanisms influencing the pathogenesis of mucormycoses, and to evaluate therapeutic strategies. This review describes the animal models established for mucormycosis, summarizes how they have been applied to study mucormycoses, and discusses the advantages and limitations of the different model systems.
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59
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Nguyen TTT, Park SW, Pangging M, Lee HB. Molecular and Morphological Confirmation of Three Undescribed Species of Mortierella from Korea. MYCOBIOLOGY 2019; 47:31-39. [PMID: 30988989 PMCID: PMC6450579 DOI: 10.1080/12298093.2018.1551854] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/03/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Three fungal isolates designated as CNUFC-YR329-1, CNUFC-PTS103-1, and CNUFC-PTS2-1 were discovered during a survey of fungal diversity of the order Mortierellales from freshwater and pine tree rhizosphere soil samples in Korea. The strains were analyzed morphologically and phylogenetically based on the internal transcribed spacer (ITS) and large subunit (LSU) of ribosomal DNA gene sequences. Based on their morphology and phylogeny, the three isolates were identified as Mortierella elongata, M. horticola, and M. humilis, respectively. To the best of our knowledge, M. elongata, M. horticola, and M. humilis, belonging to an undiscovered taxon, have not been previously described in Korea.
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Affiliation(s)
- Thuong T. T. Nguyen
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Se Won Park
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Monmi Pangging
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
- CONTACT Hyang Burm Lee
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60
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Alcalde E, Cerdá-Olmedo E, Al-Babili S. Apocarotenoids produced from β-carotene by dioxygenases from Mucor circinelloides. MICROBIOLOGY-SGM 2019; 165:433-438. [PMID: 30762519 DOI: 10.1099/mic.0.000762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mucor circinelloides exhibits the complex sexual behaviour that is induced in other Mucoromycotina by a family of apocarotenoids called trisporoids. The genome of M. circinelloides contains four genes encoding putative carotenoid cleavage dioxygenases. The gene products of two of them were sufficient to convert β-carotene into the precursors of three families of apocarotenoids, both in vitro and in the Escherichia coli heterologous in vivo system. The first of these products, CarS, cleaved the C40 β-carotene into the C15 precursor of cyclofarnesoids and a C25 apocarotenal that was converted by the second enzyme, AcaA, into the C18 precursor of trisporoids and the C7 precursor of methylhexanoids. Apocarotenoids were not found in single or mixed cultures of the two strains of opposite sex, whose interaction readily produced zygospores, the sexual fusion cells.
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Affiliation(s)
- Eugenio Alcalde
- 1School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
| | - Enrique Cerdá-Olmedo
- 2Departamento de Genética, Universidad de Sevilla, Apartado 1095, E-41080 Sevilla, Spain
| | - Salim Al-Babili
- 4Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany.,3Biological and Environmental Sciences and Engineering Division, the BioActives lab, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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61
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Pérez-Arques C, Navarro-Mendoza MI, Murcia L, Lax C, Martínez-García P, Heitman J, Nicolás FE, Garre V. Mucor circinelloides Thrives inside the Phagosome through an Atf-Mediated Germination Pathway. mBio 2019; 10:e02765-18. [PMID: 30723131 PMCID: PMC6428757 DOI: 10.1128/mbio.02765-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022] Open
Abstract
Mucormycosis is an emerging fungal infection that is often lethal due to the ineffectiveness of current therapies. Here, we have studied the first stage of this infection-the germination of Mucor circinelloides spores inside phagocytic cells-from an integrated transcriptomic and functional perspective. A relevant fungal gene network is remodeled in response to phagocytosis, being enriched in crucial functions to survive and germinate inside the phagosome, such as nutritional adaptation and response to oxidative stress. Correspondingly, the phagocytic cells induced a specific proinflammatory and apoptotic response to the pathogenic strain. Deletion of fungal genes encoding putative transcription factors (atf1, atf2, and gcn4), extracellular proteins (chi1 and pps1), and an aquaporin (aqp1) revealed that these genes perform important roles in survival following phagocytosis, germination inside the phagosome, and virulence in mice. atf1 and atf2 play a major role in these pathogenic processes, since their mutants showed the strongest phenotypes and both genes control a complex gene network of secondarily regulated genes, including chi1 and aqp1 These new insights into the initial phase of mucormycosis define genetic regulators and molecular processes that could serve as pharmacological targets.IMPORTANCE Mucorales are a group of ancient saprophytic fungi that cause neglected infectious diseases collectively known as mucormycoses. The molecular processes underlying the establishment and progression of this disease are largely unknown. Our work presents a transcriptomic study to unveil the Mucor circinelloides genetic network triggered in fungal spores in response to phagocytosis by macrophages and the transcriptional response of the host cells. Functional characterization of differentially expressed fungal genes revealed three transcription factors and three extracellular proteins essential for the fungus to survive and germinate inside the phagosome and to cause disease in mice. Two of the transcription factors, highly similar to activating transcription factors (ATFs), coordinate a complex secondary gene response involved in pathogenesis. The significance of our research is in characterizing the initial stages that lead to evasion of the host innate immune response and, in consequence, the dissemination of the infection. This genetic study offers possible targets for novel antifungal drugs against these opportunistic human pathogens.
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Affiliation(s)
- Carlos Pérez-Arques
- Departamento de Genética y Microbiología, Universidad de Murcia, Murcia, Spain
| | | | - Laura Murcia
- Departamento de Genética y Microbiología, Universidad de Murcia, Murcia, Spain
| | - Carlos Lax
- Departamento de Genética y Microbiología, Universidad de Murcia, Murcia, Spain
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Francisco E Nicolás
- Departamento de Genética y Microbiología, Universidad de Murcia, Murcia, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Universidad de Murcia, Murcia, Spain
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62
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Khuna S, Suwannarach N, Kumla J, Jomkhwan Meerak, Nuangmek W, Kiatsiriroat T, Saisamorn Lumyong. Apophysomycesthailandensis (Mucorales, Mucoromycota), a new species isolated from soil in northern Thailand and its solubilization of non-soluble minerals. MycoKeys 2019:75-92. [PMID: 30733638 PMCID: PMC6363719 DOI: 10.3897/mycokeys.45.30813] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/02/2019] [Indexed: 12/30/2022] Open
Abstract
A new species of soil fungi, described herein as Apophysomycesthailandensis, was isolated from soil in Chiang Mai Province, Thailand. Morphologically, this species was distinguished from previously described Apophysomyces species by its narrower trapezoidal sporangiospores. A physiological determination showed that A.thailandensis differs from other Apophysomyces species by its assimilation of D-turanose, D-tagatose, D-fucose, L-fucose, and nitrite. A phylogenetic analysis, performed using combined internal transcribed spacers (ITS), the large subunit (LSU) of ribosomal DNA (rDNA) regions, and a part of the histone 3 (H3) gene, lends support to our the finding that A.thailandensis is distinct from other Apophysomyces species. The genetic distance analysis of the ITS sequence supports A.thailandensis as a new fungal species. A full description, illustrations, phylogenetic tree, and taxonomic key to the new species are provided. Its metal minerals solubilization ability is reported.
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Affiliation(s)
- Surapong Khuna
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Chiang Mai University Chiang Mai Thailand.,PhD Degree Program in Applied Microbiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand University of Phayao Phayao Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Chiang Mai University Chiang Mai Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand Academy of Science, The Royal Society of Thailand Bangkok Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Chiang Mai University Chiang Mai Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand Academy of Science, The Royal Society of Thailand Bangkok Thailand
| | - Jomkhwan Meerak
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Chiang Mai University Chiang Mai Thailand
| | - Wipornpan Nuangmek
- Faculty of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand Chiang Mai University Chiang Mai Thailand
| | - Tanongkiat Kiatsiriroat
- Center of Excellence for Renewable Energy, Chiang Mai University, Chiang Mai 50200, Thailand University of Phayao Phayao Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Chiang Mai University Chiang Mai Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand Academy of Science, The Royal Society of Thailand Bangkok Thailand.,Center of Excellence for Renewable Energy, Chiang Mai University, Chiang Mai 50200, Thailand University of Phayao Phayao Thailand.,Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand Academy of Science, The Royal Society of Thailand Bangkok Thailand
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63
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Vulsteke J, Deeren D. Cutaneous mucormycosis. Transpl Infect Dis 2019; 21:e13039. [DOI: 10.1111/tid.13039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/23/2018] [Accepted: 11/21/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Dries Deeren
- Department of Hematology AZ Delta Roeselare Roeselare Belgium
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64
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Seyedmousavi S, Bosco SDMG, de Hoog S, Ebel F, Elad D, Gomes RR, Jacobsen ID, Jensen HE, Martel A, Mignon B, Pasmans F, Piecková E, Rodrigues AM, Singh K, Vicente VA, Wibbelt G, Wiederhold NP, Guillot J. Fungal infections in animals: a patchwork of different situations. Med Mycol 2018. [PMID: 29538732 DOI: 10.1093/mmy/myx104] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The importance of fungal infections in both human and animals has increased over the last decades. This article represents an overview of the different categories of fungal infections that can be encountered in animals originating from environmental sources without transmission to humans. In addition, the endemic infections with indirect transmission from the environment, the zoophilic fungal pathogens with near-direct transmission, the zoonotic fungi that can be directly transmitted from animals to humans, mycotoxicoses and antifungal resistance in animals will also be discussed. Opportunistic mycoses are responsible for a wide range of diseases from localized infections to fatal disseminated diseases, such as aspergillosis, mucormycosis, candidiasis, cryptococcosis and infections caused by melanized fungi. The amphibian fungal disease chytridiomycosis and the Bat White-nose syndrome are due to obligatory fungal pathogens. Zoonotic agents are naturally transmitted from vertebrate animals to humans and vice versa. The list of zoonotic fungal agents is limited but some species, like Microsporum canis and Sporothrix brasiliensis from cats, have a strong public health impact. Mycotoxins are defined as the chemicals of fungal origin being toxic for warm-blooded vertebrates. Intoxications by aflatoxins and ochratoxins represent a threat for both human and animal health. Resistance to antifungals can occur in different animal species that receive these drugs, although the true epidemiology of resistance in animals is unknown, and options to treat infections caused by resistant infections are limited.
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Affiliation(s)
- Seyedmojtaba Seyedmousavi
- Molecular Microbiology Section, Laboratory of Clinical Microbiology and Immunology (LCMI), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sandra de M G Bosco
- Department of Microbiology and Immunology, Institute of Biosciences-UNESP Univ Estadual Paulista Botucatu, São Paulo, Brazil
| | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, and Center of Expertise in Mycology of Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Frank Ebel
- Institut für Infektionsmedizin und Zoonosen, Munich, Germany
| | - Daniel Elad
- Department of Clinical Bacteriology and Mycology, Kimron Veterinary Institute, Veterinary Services, Ministry of Agriculture, Beit Dagan, Israel
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Graduate Programme, Curitiba Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Hans Knöll Institute, Jena, Germany
| | | | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases. Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bernard Mignon
- Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, FARAH (Fundamental and Applied Research for Animals & Health), University of Liège, Liège, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases. Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Elena Piecková
- Faculty of Medicine, Slovak Medical University, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Anderson Messias Rodrigues
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
| | - Karuna Singh
- Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
| | - Vania A Vicente
- Research Group Microbial Immunology, Hans Knöll Institute, Jena, Germany
| | - Gudrun Wibbelt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Nathan P Wiederhold
- Fungus Testing Laboratory, Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Jacques Guillot
- Department of Parasitology, Mycology and Dermatology, EA Dynamyc UPEC, EnvA, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, France
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65
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Dong Y, Sun Q, Zhang Y, Wang X, Liu P, Xiao Y, Fang Z. Complete genome of Gongronella sp. w5 provides insight into its relationship with plant. J Biotechnol 2018; 286:1-4. [DOI: 10.1016/j.jbiotec.2018.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
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66
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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67
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Lee SH, Nguyen TTT, Lee HB. Isolation and Characterization of Two Rare Mucoralean Species with Specific Habitats. MYCOBIOLOGY 2018; 46:205-214. [PMID: 30294480 PMCID: PMC6171429 DOI: 10.1080/12298093.2018.1509513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
The order Mucorales, the largest in number of species within the Mucoromycotina, comprises typically fast-growing saprotrophic fungi. During a study of the fungal diversity of undiscovered taxa in Korea, two novel mucoralean strains, CNUFC-GWD3-9 and CNUFC-EGF1-4, were isolated from specific habitats including freshwater and fecal samples, respectively. On the basis of their morphological characteristics and sequence analyses of internal transcribed spacer and large subunit ribosomal DNA, the CNUFC-GWD3-9 and CNUFC-EGF1-4 isolates were confirmed to be Gilbertella persicaria and Pilobolus crystallinus, respectively. It is ecologically, pathologically, and mycologically significant to find such rare zygomycetous fungi in such specific habitats.
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Affiliation(s)
- Seo Hee Lee
- Division of Food Technology, Biotechnology & Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Thuong T. T. Nguyen
- Division of Food Technology, Biotechnology & Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology & Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
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68
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Thielen BK, Barnes AMT, Sabin AP, Huebner B, Nelson S, Wesenberg E, Hansen GT. Widespread Lichtheimia Infection in a Patient with Extensive Burns: Opportunities for Novel Antifungal Agents. Mycopathologia 2018; 184:121-128. [PMID: 29967971 DOI: 10.1007/s11046-018-0281-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/21/2018] [Indexed: 03/04/2023]
Abstract
The Mucorales fungi-formerly classified as the zygomycetes-are environmentally ubiquitous fungi, but generally rare causes of clinical infections. In the immunocompromised host, however, they can cause invasive, rapidly spreading infections that confer a high risk of morbidity and mortality, often despite surgical and antifungal therapy. Patients with extensive burn injuries are particularly susceptible to skin and soft-tissue infections with these organisms. Here, we present a case of Lichtheimia infection in a patient with extensive full-thickness burns that required significant and repeated surgical debridement successfully treated with isavuconazole and adjunctive topical amphotericin B washes. We also review the available literature on contemporary antifungal treatment for Lichtheimia species and related Mucorales fungi.
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Affiliation(s)
- Beth K Thielen
- Department of Medicine (Division of Infectious Diseases and International Medicine), University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA. .,Department of Pediatrics (Division of Pediatric Infectious Diseases and Immunology), University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA.
| | - Aaron M T Barnes
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA.,Department of Microbiology & Immunology, University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA
| | - Arick P Sabin
- Department of Medicine (Division of Infectious Diseases and International Medicine), University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA
| | - Becky Huebner
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, Minneapolis, MN, 55415, USA
| | - Susan Nelson
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, Minneapolis, MN, 55415, USA
| | - Elizabeth Wesenberg
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, Minneapolis, MN, 55415, USA
| | - Glen T Hansen
- Department of Medicine (Division of Infectious Diseases and International Medicine), University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, 55455, USA.,Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, Minneapolis, MN, 55415, USA
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69
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Zhang TY, Yu Y, Zhu H, Yang SZ, Yang TM, Zhang MY, Zhang YX. Absidia panacisoli sp. nov., isolated from rhizosphere of Panax notoginseng. Int J Syst Evol Microbiol 2018; 68:2468-2472. [PMID: 29927367 DOI: 10.1099/ijsem.0.002857] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain (SYPF 7183T) was isolated from rhizosphere soil of Panax notoginseng in southwest China. Phylogenetic analyses indicated that strain SYPF 7183T was distinct from the other Absidia species with well-supported values. Strain SYPF 7183T produced spherical or subpyriform sporangia and short cylindrical sporangiospores. The azygospores were globose to oval. Based on morphological and phylogenetic evidence, the novel strain Absidia panacisoli sp. nov. is proposed.
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Affiliation(s)
- Tian-Yuan Zhang
- 1School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Ying Yu
- 1School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - He Zhu
- 1School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Shao-Zhou Yang
- 2Wenshan Sanqi Research Institute, Wenshan University, Wenshan, 663000, PR China.,3Wenshan Miaoxiang Notoginseng Industrial Co. Ltd, Wenshan, 663000, PR China
| | - Tian-Mei Yang
- 4Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, 650200, PR China
| | - Meng-Yue Zhang
- 1School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Yi-Xuan Zhang
- 1School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
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70
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Abstract
Purpose of review Mucormycosis is an emerging opportunistic fungal infection whose causative agents are found within the Mucorales family. A recent increase in immunocompromised cohorts with solid organ transplants, diabetes mellitus, and other medical conditions have resulted in increased fungal infections including mucormycosis. Our current knowledge about Mucoralean fungi is in its infancy compared to other fungal pathogens, which may be due to lack of robust genetic tools for Mucorales. In this review we summarize recent advances in genetic tools to study the two most prevalent and genetically amenable Mucoralean fungi, Mucor circinelloides and Rhizopus delemar. Recent findings There have been advances made in the study of Mucorales family genetics. These findings include the construction of recyclable markers to manipulate the genome, as well as silencing vectors, and the adaptation of the CRISPR/Cas9 gene editing system. Summary We present how these genetic methods have been applied to understand basic biology, morphogenesis, pathogenesis, and host-pathogen interactions in the two Mucoralean fungi, M. circinelloides and R. delemar. With these advances in Mucorales the opportunity to further understand the pathogenesis of these organisms is opened.
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71
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Abstract
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.
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Abstract
The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.
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73
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Diversity of mucoralean fungi in soils of papaya (Carica papaya L.) producing regions in Mexico. Fungal Biol 2018; 122:810-816. [PMID: 30007431 DOI: 10.1016/j.funbio.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 11/22/2022]
Abstract
Mexico is the fifth largest producer of papaya worldwide and has recently reported problems with mucoralean fungi in this crop. These fungi are considered saprophytes in the soil and are ubiquitous in nature. In this work, they were isolated from soil in regions of intensive papaya cultivation in Mexico. Collections were made in the states of Colima, Oaxaca and Veracruz in Apr 2016. A total of 72 mucorales fungal isolates was obtained and morphologically characterized and then molecular characterization (28S ribosomal region) of 25 representative isolates was carried out. Phylogenetic analysis of the sequences confirmed the presence of the species Gilbertella persicaria, Rhizopus oryzae, Rhizopus stolonifer, Mucor circinelloides and Mucor hiemalis, which cause soft rot in papaya fruits, therefore, spores of these fungi found in the orchard soils can be considered as a constant source of contamination that affects healthy fruits. Additionally, Choanephora cucurbitarum, Mucor ellipsoideus, Rhizopus homothallicus, Rhizopus microsporus, Rhizopus schipperae, Lichteimia ramosa, Gongronella butleri, Cunninghamella bertholletiae and Cunninghamella blakesleeana were identified which are considered to have agricultural, biotechnological and medical importance.
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74
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Albert Q, Leleyter L, Lemoine M, Heutte N, Rioult JP, Sage L, Baraud F, Garon D. Comparison of tolerance and biosorption of three trace metals (Cd, Cu, Pb) by the soil fungus Absidia cylindrospora. CHEMOSPHERE 2018; 196:386-392. [PMID: 29316464 DOI: 10.1016/j.chemosphere.2017.12.156] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/16/2017] [Accepted: 12/22/2017] [Indexed: 05/27/2023]
Abstract
Trace metals cause deterioration of the soil and constitute a major concern for the environment and human health. Bioremediation could be an effective solution for the rectification of contaminated soils. Fungi could play an important role in biodegradation because of the morphology of their mycelium (highly reactive and extensive biological surface) and its physiology (high tolerance to many stresses, production of enzymes and secondary metabolites). Fungi can effectively biosequestrate, or biotransform many organic and inorganic contaminants into a non-bioavailable form. This experiment was designed to evaluate the tolerance and the biosorption abilities of the fungus Absidia cylindrospora against three trace metals: Cadmium (Cd), Copper (Cu), and Lead (Pb). Firstly, the tolerance of the strain was evaluated on metal-enriched malt extract agar (MEA). Secondly, the strain was exposed to trace metals, in a liquid malt extract medium. After 3 or 7 days of exposure, the quantities of absorbed and adsorbed metals were measured with Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES). Biomass production and pH evolution were also evaluated during the test. Our experiment revealed differences between the three metals. In agar medium, Cd and Pb were better tolerated than Cu. In liquid medium, Cd and Pb were mostly absorbed whereas Cu was mostly adsorbed. A. cylindrospora biosorbed 14% of Cu, 59% of Pb and 68% of Cd when exposed for 3 days at 50 mg L-1.
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Affiliation(s)
- Quentin Albert
- Normandie Univ, UNICAEN, ABTE EA 4651, Centre F. Baclesse, 14000, Caen, France
| | - Lydia Leleyter
- Normandie Univ, UNICAEN, ABTE EA 4651, Centre F. Baclesse, 14000, Caen, France
| | - Mélanie Lemoine
- Normandie Univ, UNICAEN, ABTE EA 4651, Centre F. Baclesse, 14000, Caen, France
| | - Natacha Heutte
- Normandie Univ, UNIROUEN, CETAPS EA3 832, 76821, Mont Saint Aignan Cedex, France
| | | | - Lucile Sage
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS / USMB Université Grenoble Alpes, 38058, Grenoble, Cedex 9, France
| | - Fabienne Baraud
- Normandie Univ, UNICAEN, ABTE EA 4651, Centre F. Baclesse, 14000, Caen, France
| | - David Garon
- Normandie Univ, UNICAEN, ABTE EA 4651, Centre F. Baclesse, 14000, Caen, France.
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75
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Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0395-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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76
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Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O'Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 2018; 108:1028-1046. [PMID: 27738200 DOI: 10.3852/16-042] [Citation(s) in RCA: 628] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/04/2016] [Indexed: 12/12/2022]
Abstract
Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.
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Affiliation(s)
- Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611
| | - Katy Lazarus
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611
| | - Mary L Berbee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, K1N 6N5 Canada
| | - Igor Grigoriev
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598
| | | | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48103
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, NCAUR-ARS-USDA, 1815 N. University Street, Peoria, Illinois 61604
| | - Robert W Roberson
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Thomas N Taylor
- Department of Ecology and Evolutionary Biology, and Natural History Museum and Biodiversity Research Center, University of Kansas, Lawrence, Kansas 66045
| | - Jessie Uehling
- Biology Department, Box 90338, Duke University, Durham, North Carolina 27708
| | - Rytas Vilgalys
- Biology Department, Box 90338, Duke University, Durham, North Carolina 27708
| | - Merlin M White
- Department of Biological Sciences, Boise State University, Boise, Idaho 83725
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California 92521
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77
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Nguyen TTT, Lee HB. Isolation and Characterization of Three Zygomycetous Fungi in Korea: Backusella circina, Circinella muscae, and Mucor ramosissimus. MYCOBIOLOGY 2018; 46:317-327. [PMID: 30637140 PMCID: PMC6319469 DOI: 10.1080/12298093.2018.1538071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 05/05/2023]
Abstract
While surveying undiscovered fungal taxa in Korea, three rare zygomycetous fungal strains, CNUFC-PTF2-1, CNUFC-TF3-1, and CNUFC-ESAF3-1, were isolated from soil, leaf, and freshwater samples, respectively. The strains were analyzed morphologically as well as phylogenetically based on the internal transcribed spacer region and 28S rDNA sequences. Sequence analysis of the two loci revealed that the isolates, CNUFC-PTF2-1, CNUFC-TF3-1, and CNUFC-ESAF3-1, were identified as Backusella circina, Circinella muscae, and Mucor ramosissimus, respectively. These species have not yet been previously described in Korea.
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Affiliation(s)
- Thuong T T Nguyen
- Division of Food Technology, Biotechnology & Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology & Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
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78
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Satari B, Karimi K. Mucoralean fungi for sustainable production of bioethanol and biologically active molecules. Appl Microbiol Biotechnol 2017; 102:1097-1117. [DOI: 10.1007/s00253-017-8691-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 11/27/2022]
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79
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Caramalho R, Tyndall JDA, Monk BC, Larentis T, Lass-Flörl C, Lackner M. Intrinsic short-tailed azole resistance in mucormycetes is due to an evolutionary conserved aminoacid substitution of the lanosterol 14α-demethylase. Sci Rep 2017; 7:15898. [PMID: 29162893 PMCID: PMC5698289 DOI: 10.1038/s41598-017-16123-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/08/2017] [Indexed: 11/24/2022] Open
Abstract
Mucormycoses are emerging and potentially lethal infections. An increase of breakthrough infections has been found in cohorts receiving short-tailed azoles prophylaxis (e.g. voriconazole (VCZ)). Although VCZ is ineffective in vitro and in vivo, long-tailed triazoles such as posaconazole remain active against mucormycetes. Our goal was to validate the molecular mechanism of resistance to short-tailed triazoles in Mucorales. The paralogous cytochrome P450 genes (CYP51 F1 and CYP51 F5) of Rhizopus arrhizus, Rhizopus microsporus, and Mucor circinelloides were amplified and sequenced. Alignment of the protein sequences of the R. arrhizus, R. microsporus, and M. circinelloides CYP51 F1 and F5 with additional Mucorales species (n = 3) and other fungi (n = 16) confirmed the sequences to be lanosterol 14α-demethylases (LDMs). Sequence alignment identified a pan-Mucorales conservation of a phenylalanine129 substitution in all CYP51 F5s analyzed. A high resolution X-ray crystal structure of Saccharomyces cerevisiae LDM in complex with VCZ was used for generating a homology model of R. arrhizus CYP51 F5. Structural and functional knowledge of S. cerevisiae CYP51 shows that the F129 residue in Mucorales CYP51 F5 is responsible for intrinsic resistance of Mucorales against short-tailed triazoles, with a V to A substitution in Helix I also potentially playing a role.
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Affiliation(s)
- Rita Caramalho
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße, number 41, 2nd floor, A-6020, Innsbruck, Austria
| | - Joel D A Tyndall
- School of Pharmacy, University of Otago, Dunedin, 9054, New Zealand
| | - Brian C Monk
- Sir John Walsh Research Institute and the Department of Oral Sciences, New Zealand's National Centre for Dentistry, University of Otago, Dunedin, 9054, New Zealand
| | - Thomas Larentis
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße, number 41, 2nd floor, A-6020, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße, number 41, 2nd floor, A-6020, Innsbruck, Austria
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße, number 41, 2nd floor, A-6020, Innsbruck, Austria.
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80
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Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales. BMC Genomics 2017; 18:736. [PMID: 28923009 PMCID: PMC5604411 DOI: 10.1186/s12864-017-4136-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/08/2017] [Indexed: 12/28/2022] Open
Abstract
Background Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism. Results The whole genome of A. variabilis NCCPF 102052 was sequenced and the genomic structure of A. variabilis was compared with already available genome structures of A. elegans, A. trapeziformis and other medically important Mucorales. The total size of genome assembly of A. variabilis was 39.38 Mb with 12,764 protein-coding genes. The transposable elements (TEs) were low in Apophysomyces genome and the retrotransposon Ty3-gypsy was the common TE. Phylogenetically, Apophysomyces species were grouped closely with Phycomyces blakesleeanus. OrthoMCL analysis revealed 3025 orthologues proteins, which were common in those three pathogenic Apophysomyces species. Expansion of multiple gene families/duplication was observed in Apophysomyces genomes. Approximately 6% of Apophysomyces genes were predicted to be associated with virulence on PHIbase analysis. The virulence determinants included the protein families of CotH proteins (invasins), proteases, iron utilisation pathways, siderophores and signal transduction pathways. Serine proteases were the major group of proteases found in all Apophysomyces genomes. The carbohydrate active enzymes (CAZymes) constitute the majority of the secretory proteins. Conclusion The present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis. Together with available genome sequence of A. elegans and A. trapeziformis, the study helped to indicate the possible virulence determinants of pathogenic Apophysomyces species. The presence of unique CAZymes in cell wall might be exploited in future for antifungal drug development. Electronic supplementary material The online version of this article (10.1186/s12864-017-4136-1) contains supplementary material, which is available to authorized users.
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Abstract
Although at the level of resolution of genes and molecules most information about mating in fungi is from a single lineage, the Dikarya, many fundamental discoveries about mating in fungi have been made in the earlier branches of the fungi. These are nonmonophyletic groups that were once classified into the chytrids and zygomycetes. Few species in these lineages offer the potential of genetic tractability, thereby hampering the ability to identify the genes that underlie those fundamental insights. Research performed during the past decade has now established the genes required for mating type determination and pheromone synthesis in some species in the phylum Mucoromycota, especially in the order Mucorales. These findings provide striking parallels with the evolution of mating systems in the Dikarya fungi. Other discoveries in the Mucorales provide the first examples of sex-cell type identity being driven directly by a gene that confers mating type, a trait considered more of relevance to animal sex determination but difficult to investigate in animals. Despite these discoveries, there remains much to be gleaned about mating systems from these fungi.
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Lazarus KL, Benny GL, Ho HM, Smith ME. Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina), a genus of ubiquitous mycoparasites. Mycologia 2017; 109:333-349. [PMID: 28489971 DOI: 10.1080/00275514.2017.1307005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We examined phylogenetic relationships among species of the mycoparasite genus Syncephalis using sequences from three nuclear ribsosomal DNA genes (18S, 5.8S, and 28S nuc rDNA) and a gene encoding the largest subunit of RNA polymerase II (RPB1). Our data set included 88 Syncephalis isolates comprising 23 named species and several unnamed taxa. We also revived a culturing technique using beef liver and cellophane to grow several Syncephalis isolates without their host fungi to obtain pure parasite DNA. Most isolates, however, were grown in co-cultures with their host fungi, so we designed Syncephalis-specific primers to obtain sequence data. Individual and combined data sets were analyzed by maximum likelihood (ML) and Bayesian methods. We recovered 20 well-supported lineages and 38 operational taxonomic units (OTUs). Most major clades contained isolates from distant localities on multiple continents. There were taxonomic and nomenclature issues within several clades, probably due to high phenotypic plasticity or species dimorphism. We also conducted an analysis of Syncephalis nuc rDNA internal transcribed spacer (ITS) sequences for 31 phylogenetically diverse isolates, and we determined that most Syncephalis species have long ITS sequences relative to other fungi. Although commonly employed eukaryotic and fungal primers are compatible with diverse Syncephalis species, the ITS sequences of Syncepahlis are nonetheless rarely recovered in environmental molecular diversity surveys.
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Affiliation(s)
- Katherine L Lazarus
- a Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Gerald L Benny
- a Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Hsiao-Man Ho
- b Department of Science Education , National Taipei University of Education , 134, Sect. 2, Heping E. Road, Taipei 106 , Taiwan
| | - Matthew E Smith
- a Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
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Yacoub A, Soni KK, Mojica L, Mai J, Morano J, Cruse CW, Sandin RL, Nanjappa S, Bohra C, Gajanan G, Greene JN. Primary Gangrenous Cutaneous Mold Infections in a Patient With Cancer and Neutropenia. Cancer Control 2017; 23:265-71. [PMID: 27556666 DOI: 10.1177/107327481602300309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Opportunistic fungal infections caused by Aspergillus and Candida followed by infections with Fusarium, Rhizopus, Mucor, and Alternaria species are an important cause of morbidity and mortality in patients with hematological malignancies. Cutaneous mucormycosis infections are rare, and the incidence, outcomes, and factors associated with survival in the setting of hematological malignancies are not clear. METHODS A literature search was conducted for all cases of primary cutaneous mold infections in patients with hematological malignancy, of which 50 cases were found. Our case of a patient with a hematological malignancy who sustained a cat bite that in turn caused a primary cutaneous mold infection is also included. RESULTS In the 51 cases identified, 66.7% were neutropenic upon presentation, and 54.9% were male with an average age of 32 years. Aspergillus species (33.3%) was the most cited followed by Rhizopus species (19.6%). Overall mortality rate was 29.4% and was observed more frequently in patients with neutropenia (60.0%) and without surgical intervention (73.3%). Survival rate was higher (35.3%) for cases utilizing both antifungal and surgical intervention. The antifungal agent with the highest survival rate was amphotericin B and its formulations (58.8%). CONCLUSIONS Neutropenia within hematological malignancies demonstrate a risk for developing severe cutaneous fungal infections, of which primary cutaneous mucormycosis can carry significant mortality. Combination antifungal therapy and surgical debridement appears to be associated with higher survival outcomes and warrants further investigation.
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Affiliation(s)
- Abraham Yacoub
- Department of Infectious Diseases and Tropical Medicine, Moffitt Cancer Center, Tampa, FL 33612, USA.
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Hérivaux A, Dugé de Bernonville T, Roux C, Clastre M, Courdavault V, Gastebois A, Bouchara JP, James TY, Latgé JP, Martin F, Papon N. The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by Fungi. mBio 2017; 8:e01739-16. [PMID: 28143977 PMCID: PMC5285503 DOI: 10.1128/mbio.01739-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Histidine kinases (HKs) are among the most prominent sensing proteins studied in the kingdom Fungi. Their distribution and biological functions in early diverging fungi (EDF), however, remain elusive. We have taken advantage of recent genomic resources to elucidate whether relationships between the occurrence of specific HKs in some EDF and their respective habitat/lifestyle could be established. This led to the unexpected discovery of fungal HKs that share a high degree of similarity with receptors for plant hormones (ethylene and cytokinin). Importantly, these phytohormone receptor homologs are found not only in EDF that behave as plant root symbionts or endophytes but also in EDF species that colonize decaying plant material. We hypothesize that these particular sensing proteins promoted the interaction of EDF with plants, leading to the conquest of land by these ancestral fungi.
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Affiliation(s)
- Anaïs Hérivaux
- Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, Angers, France
| | - Thomas Dugé de Bernonville
- Université François-Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales, Tours, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Castanet-Tolosan, France
| | - Marc Clastre
- Université François-Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales, Tours, France
| | - Vincent Courdavault
- Université François-Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales, Tours, France
| | - Amandine Gastebois
- Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, Angers, France
| | | | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jean-Paul Latgé
- Institut Pasteur de Paris, Unité des Aspergillus, Paris, France
| | - Francis Martin
- Institut National de la Recherche Agronomique, Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Nancy, France
| | - Nicolas Papon
- Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, Angers, France
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Trieu TA, Navarro-Mendoza MI, Pérez-Arques C, Sanchis M, Capilla J, Navarro-Rodriguez P, Lopez-Fernandez L, Torres-Martínez S, Garre V, Ruiz-Vázquez RM, Nicolás FE. RNAi-Based Functional Genomics Identifies New Virulence Determinants in Mucormycosis. PLoS Pathog 2017; 13:e1006150. [PMID: 28107502 PMCID: PMC5287474 DOI: 10.1371/journal.ppat.1006150] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 02/01/2017] [Accepted: 12/22/2016] [Indexed: 01/17/2023] Open
Abstract
Mucorales are an emerging group of human pathogens that are responsible for the lethal disease mucormycosis. Unfortunately, functional studies on the genetic factors behind the virulence of these organisms are hampered by their limited genetic tractability, since they are reluctant to classical genetic tools like transposable elements or gene mapping. Here, we describe an RNAi-based functional genomic platform that allows the identification of new virulence factors through a forward genetic approach firstly described in Mucorales. This platform contains a whole-genome collection of Mucor circinelloides silenced transformants that presented a broad assortment of phenotypes related to the main physiological processes in fungi, including virulence, hyphae morphology, mycelial and yeast growth, carotenogenesis and asexual sporulation. Selection of transformants with reduced virulence allowed the identification of mcplD, which encodes a Phospholipase D, and mcmyo5, encoding a probably essential cargo transporter of the Myosin V family, as required for a fully virulent phenotype of M. circinelloides. Knock-out mutants for those genes showed reduced virulence in both Galleria mellonella and Mus musculus models, probably due to a delayed germination and polarized growth within macrophages. This study provides a robust approach to study virulence in Mucorales and as a proof of concept identified new virulence determinants in M. circinelloides that could represent promising targets for future antifungal therapies. Mucormycosis is an infectious disease caused by organisms of the order Mucorales. It is a lethal infection that is raising the alarm in the medical and scientific community due to its high mortality rates, unusual antifungal drug resistance and its emerging character. Among the reasons explaining the nescience about this disease is the lack of knowledge on the biology of the organisms that cause mucormycosis, which is encouraged by the reluctance of these species to genetic studies. In this work, we have developed an RNAi-based functional genomic platform to study virulence in Mucorales. It is a powerful tool available for the scientific community that will contribute to solve the reluctance of Mucorales to genetic studies and will help to understand the genetic basis of virulence in these organisms. Secondly, and as a proof of concept, we have used this genetic tool to identify two new virulence determinants in Mucor circinelloides. Lack of function of these determinants delays germination and growth of spores, conceding time to macrophages for the inactivation of the pathogen. The two genes identified, mcplD and mcmyo5, represent promising targets for future development of new antifungal therapies against mucormycosis.
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Affiliation(s)
- Trung Anh Trieu
- Departmento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain
| | | | - Carlos Pérez-Arques
- Departmento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain
| | - Marta Sanchis
- Unidad de Microbiología, Universitat Rovira i Virgili, IISPV, Tarragona, Spain
| | - Javier Capilla
- Unidad de Microbiología, Universitat Rovira i Virgili, IISPV, Tarragona, Spain
| | | | | | | | - Victoriano Garre
- Departmento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain
| | | | - Francisco E. Nicolás
- Departmento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain
- * E-mail:
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Ellenberger S, Burmester A, Schuster S, Wöstemeyer J. Post-translational regulation by structural changes of 4-dihydromethyltrisporate dehydrogenase, a key enzyme in sexual and parasitic communication mediated by the trisporic acid pheromone system, of the fungal fusion parasite Parasitella parasitica. J Theor Biol 2017; 413:50-57. [DOI: 10.1016/j.jtbi.2016.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/05/2016] [Indexed: 12/17/2022]
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88
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Morin-Sardin S, Nodet P, Coton E, Jany JL. Mucor: A Janus-faced fungal genus with human health impact and industrial applications. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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89
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Ellenberger S, Burmester A, Wöstemeyer J. The fate of mitochondria after infection of the Mucoralean fungus Absidia glauca by the fusion parasite Parasitella parasitica: comparison of mitochondrial genomes in zygomycetes. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:113-120. [PMID: 28034347 DOI: 10.1080/24701394.2016.1248432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Absidia glauca and Parasitella parasitica constitute a versatile experimental system for studying horizontal gene transfer between a mucoralean host and its fusion parasite. The A. glauca chondriome has a length of approximately 63 kb and a GC content of 28%. The chondriome of P. parasitica is larger, 83 kb, and contains 31% GC base pairs. These mtDNAs contain the standard fungal mitochondrial gene set, small and large subunit rRNAs, plus ribonuclease P RNA. Comparing zygomycete chondriomes reveals an unusually high number of homing endonuclease genes in P. parasitica, substantiating the mobility of intron elements independent of host-parasite interactions.
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Affiliation(s)
- Sabrina Ellenberger
- a Chair for General Microbiology and Microbe Genetics , Friedrich Schiller University Jena , Jena , Germany
| | - Anke Burmester
- a Chair for General Microbiology and Microbe Genetics , Friedrich Schiller University Jena , Jena , Germany
| | - Johannes Wöstemeyer
- a Chair for General Microbiology and Microbe Genetics , Friedrich Schiller University Jena , Jena , Germany
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Diaz PI, Hong BY, Dupuy AK, Strausbaugh LD. Mining the oral mycobiome: Methods, components, and meaning. Virulence 2016; 8:313-323. [PMID: 27791473 DOI: 10.1080/21505594.2016.1252015] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly. Some taxa such as Malassezia, however, appear in high prevalence and abundance in molecular studies but have not been cultivated. Important technical and bioinformatic challenges to ITS-based oral mycobiome studies are discussed. These include optimization of sample lysis, variability in length of ITS amplicons, high intra-species ITS sequence variability, high inter-species variability in ITS copy number and challenges in nomenclature and maintenance of curated reference databases. Molecular surveys are powerful first steps to characterize the oral mycobiome but further research is needed to unravel which fungi detected by DNA are true oral residents and what role they play in oral homeostasis.
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Affiliation(s)
- Patricia I Diaz
- a Division of Periodontology, Department of Oral Health and Diagnostic Sciences , School of Dental Medicine, UConn Health , Farmington , CT , USA
| | - Bo-Young Hong
- a Division of Periodontology, Department of Oral Health and Diagnostic Sciences , School of Dental Medicine, UConn Health , Farmington , CT , USA
| | - Amanda K Dupuy
- b Institute for Systems Genomics, University of Connecticut , Storrs , CT , USA
| | - Linda D Strausbaugh
- b Institute for Systems Genomics, University of Connecticut , Storrs , CT , USA
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Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM. An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun 2016; 7:12218. [PMID: 27447865 PMCID: PMC4961843 DOI: 10.1038/ncomms12218] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/09/2016] [Indexed: 12/22/2022] Open
Abstract
Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets.
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Affiliation(s)
- Marcus C. Chibucos
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sameh Soliman
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Teclegiorgis Gebremariam
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Hongkyu Lee
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Sean Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Tracy H. Hazen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kizee A. Etienne
- Fungal Reference Laboratory, Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David A. Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California 90502, USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Shawn R. Lockhart
- Fungal Reference Laboratory, Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher D. Skory
- National Center for Agriculture Utilization Research, USDA, Agricultural Research Service, Peoria, Illinois 61604, USA
| | - Ashraf S. Ibrahim
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California 90502, USA
| | - Vincent M. Bruno
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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Pawłowska J, Aleksandrzak-Piekarczyk T, Banach A, Kiersztyn B, Muszewska A, Serewa L, Szatraj K, Wrzosek M. Preliminary studies on the evolution of carbon assimilation abilities within Mucorales. Fungal Biol 2016; 120:752-63. [DOI: 10.1016/j.funbio.2016.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/01/2022]
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Ziaee A, Zia M, Bayat M, Hashemi J. Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes. Jundishapur J Microbiol 2016; 9:e35237. [PMID: 27284399 PMCID: PMC4898167 DOI: 10.5812/jjm.35237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/18/2022] Open
Abstract
Background The Mucorales are an important opportunistic fungi that can cause mucormycosis in immunocompromised patients. The fast and precise diagnosis of mucormycosis is very important because, if the diagnosis is not made early enough, dissemination often occurs. It is now well established that molecular methods such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) are feasible and reliable tools for the early and accurate diagnosis of mucormycosis agents. Objectives The present study was conducted to evaluate the validity of PCR-RFLP for the identification of Mucorales and some important Mucor and Lichtheimia species in pure cultures of Zygomycetes. Materials and Methods Specific sense and anti-sense primers were used to amplify the Mucorales, Mucor, and Lichtheimia DNA. The PCR products were digested by AfIII, XmnI, and AcII restriction enzymes, and the resultant restriction pattern was analyzed. Results On the basis of the molecular and morphological data, we identified Mucor plumbeus (10.83%), M. circinelloides (9.17%), Lichtheimia corymbifera (9.17%), M. racemosus (5.83%), M. ramosissimus (3.33%), and L. blakesleeana (0.83%). Conclusions It seems that PCR-RFLP is a suitable technique for the identification of Mucorales at the species level.
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Affiliation(s)
- Ardeshir Ziaee
- Department of Medical and Veterinary Mycology, Faculty of Veterinary Specialized Sciences, Science and Research Branch, Islamic Azad University, Tehran, IR Iran
| | - Mohammadali Zia
- Department of Basic Sciences, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, IR Iran
- Corresponding author: Mohammadali Zia, Department of Basic Sciences, Khorasgan (Isfahan) Branch, Islamic Azad University, Isfahan, IR Iran. Tel: +98-9133094852, E-mail:
| | - Mansour Bayat
- Department of Medical and Veterinary Mycology, Faculty of Veterinary Specialized Sciences, Science and Research Branch, Islamic Azad University, Tehran, IR Iran
| | - Jamal Hashemi
- Department of Medical Parasitology and Mycology, Institute of Public Health Research, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
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Kaerger K, Schwartze VU, Dolatabadi S, Nyilasi I, Kovács SA, Binder U, Papp T, Hoog SD, Jacobsen ID, Voigt K. Adaptation to thermotolerance in Rhizopus coincides with virulence as revealed by avian and invertebrate infection models, phylogeny, physiological and metabolic flexibility. Virulence 2016; 6:395-403. [PMID: 26065324 DOI: 10.1080/21505594.2015.1029219] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Mucormycoses are fungal infections caused by the ancient Mucorales. They are rare, but increasingly reported. Predisposing conditions supporting and favoring mucormycoses in humans and animals include diabetic ketoacidosis, immunosuppression and haematological malignancies. However, comprehensive surveys to elucidate fungal virulence in ancient fungi are limited and so far focused on Lichtheimia and Mucor. The presented study focused on one of the most important causative agent of mucormycoses, the genus Rhizopus (Rhizopodaceae). All known clinically-relevant species are thermotolerant and are monophyletic. They are more virulent compared to non-clinically, mesophilic species. Although adaptation to elevated temperatures correlated with the virulence of the species, mesophilic strains showed also lower virulence in Galleria mellonella incubated at permissive temperatures indicating the existence of additional factors involved in the pathogenesis of clinical Rhizopus species. However, neither specific adaptation to nutritional requirements nor stress resistance correlated with virulence, supporting the idea that Mucorales are predominantly saprotrophs without a specific adaptation to warm blooded hosts.
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Nguyen TTT, Lee SH, Bae S, Jeon SJ, Mun HY, Lee HB. Characterization of Two New Records of Zygomycete Species Belonging to Undiscovered Taxa in Korea. MYCOBIOLOGY 2016; 44:29-37. [PMID: 27103852 PMCID: PMC4838589 DOI: 10.5941/myco.2016.44.1.29] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 03/25/2016] [Accepted: 03/27/2016] [Indexed: 05/10/2023]
Abstract
During a biodiversity survey of undiscovered taxa in Korea, two zygomycetous fungal strains were isolated. The first strain, EML-FSDY6-1 was isolated from a soil sample collected at Dokdo Island in the East Sea of Korea in 2013, and the second strain, EML-DG-NH3-1 was isolated from a rat dung sample collected at Chonnam National University garden, Gwangju, Korea in 2014. Based on the morphological characteristics and phylogenetic analysis of the internal transcribed spacer, 18S and 28S rDNA, actin and translation elongation factor-1α genes. EML-FSDY6-1 and EML-DG-NH3-1 isolates were confirmed as zygomycete species, Absidia pseudocylindrospora and Absidia glauca, respectively. Neither species has previously been described in Korea.
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Affiliation(s)
- Thi Thuong Thuong Nguyen
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Seo Hee Lee
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Sarah Bae
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Sun Jeong Jeon
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Hye Yeon Mun
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea.; Microbial Safety Division, NAAS-RDA, Wanju 55365, Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
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97
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Benny GL, Smith ME, Kirk PM, Tretter ED, White MM. Challenges and Future Perspectives in the Systematics of Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina. BIOLOGY OF MICROFUNGI 2016. [DOI: 10.1007/978-3-319-29137-6_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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98
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Voglmayr H, Clémençon H. Identification and taxonomic position of two mucoralean endoparasites of Hysterangium (Basidiomycota) based on molecular and morphological data. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1150-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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99
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Levetin E, Horner WE, Scott JA. Taxonomy of Allergenic Fungi. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2015; 4:375-385.e1. [PMID: 26725152 DOI: 10.1016/j.jaip.2015.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/16/2015] [Indexed: 12/11/2022]
Abstract
The Kingdom Fungi contains diverse eukaryotic organisms including yeasts, molds, mushrooms, bracket fungi, plant rusts, smuts, and puffballs. Fungi have a complex metabolism that differs from animals and plants. They secrete enzymes into their surroundings and absorb the breakdown products of enzyme action. Some of these enzymes are well-known allergens. The phylogenetic relationships among fungi were unclear until recently because classification was based on the sexual state morphology. Fungi lacking an obvious sexual stage were assigned to the artificial, now-obsolete category, "Deuteromycetes" or "Fungi Imperfecti." During the last 20 years, DNA sequencing has resolved 8 fungal phyla, 3 of which contain most genera associated with important aeroallergens: Zygomycota, Ascomycota, and Basidiomycota. Advances in fungal classification have required name changes for some familiar taxa. Because of regulatory constraints, many fungal allergen extracts retain obsolete names. A major benefit from this reorganization is that specific immunoglobulin E (IgE) levels in individuals sensitized to fungi appear to closely match fungal phylogenetic relationships. This close relationship between molecular fungal systematics and IgE sensitization provides an opportunity to systematically look at cross-reactivity and permits representatives from each taxon to serve as a proxy for IgE to the group.
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Affiliation(s)
- Estelle Levetin
- Faculty of Biological Science, University of Tulsa, Tulsa, Okla.
| | | | - James A Scott
- Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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100
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Diversity, ecology, and evolution in Phycomyces. Fungal Biol 2015; 119:1007-1021. [DOI: 10.1016/j.funbio.2015.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 07/02/2015] [Accepted: 07/14/2015] [Indexed: 12/17/2022]
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