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Hoang MTV, Irinyi L, Chen SCA, Sorrell TC, Meyer W. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections. Front Microbiol 2019; 10:1647. [PMID: 31379792 PMCID: PMC6657352 DOI: 10.3389/fmicb.2019.01647] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022] Open
Abstract
Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Sharon C. A. Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C. Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
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102
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Zhang WH, Sun RB, Xu L, Liang JN, Wu TY, Zhou J. Effects of micro-/nano-hydroxyapatite and phytoremediation on fungal community structure in copper contaminated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:100-109. [PMID: 30822666 DOI: 10.1016/j.ecoenv.2019.02.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/03/2019] [Accepted: 02/14/2019] [Indexed: 05/04/2023]
Abstract
Micro-/nano-hydroxyapatite (MHA/NHA) has been used to reduce the concentration of available heavy metals and increase soil pH in the remediation of heavy metal-contaminated soils. However, little is known about the effects of MHA and NHA on soil fungal communities and function. In this study, fungal community composition was characterized from copper-contaminated soils amended with MHA, NHA and three other classic amendments combined with Elsholtzia splendens during a 3-year immobilization experiment. High-throughput sequencing results showed that applications of MHA increased the richness and diversity of the fungal community, which was opposite the results of NHA. SIMPER analysis indicated that both the relative abundance of fungi associated with biosorption and plant growth promotion increased, whereas the relative abundance of fungi related to bioleaching and potential pathogens decreased after applying MHA. Redundancy (RDA) analysis revealed that the soil pH was a crucial environmental factor in the succession of fungal communities. In addition, the results of functional prediction via FUNGuild suggested that the application of MHA had the potential to reduce the risk of pathogens infecting animals and plants in the soil but that NHA had some environmental risks. Overall, fungal community showed a synergistic effect of immobilization with the test amendments, and MHA was better for the remediation of heavy metal-contaminated soils than the other test amendments.
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Affiliation(s)
- Wen-Hui Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment station, Chinese Academy of Sciences, Liujiazhan plantation, Yingtan 335211, China
| | - Rui-Bo Sun
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Lei Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment station, Chinese Academy of Sciences, Liujiazhan plantation, Yingtan 335211, China
| | - Jia-Ni Liang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Tian-Yi Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment station, Chinese Academy of Sciences, Liujiazhan plantation, Yingtan 335211, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment station, Chinese Academy of Sciences, Liujiazhan plantation, Yingtan 335211, China; Jiangxi Engineering Research Center of Eco-Remediation of Heavy Metal Pollution, Jiangxi Academy of Science, Nanchang 330096, China.
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103
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Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G. PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 2019; 53:73-91. [PMID: 31205446 PMCID: PMC6557899 DOI: 10.3897/mycokeys.53.34761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022] Open
Abstract
The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities.
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Affiliation(s)
- Cécile Gueidan
- Australian National Herbarium, National Research Collections Australia, CSIRO-NCMI, Canberra, ACT, 2601, Australia Australian National Herbarium Canberra Australia
| | - John A Elix
- Research School of Chemistry, Building 137, Australian National University, Canberra, ACT, 2601, Australia Australian National University Canberra Australia
| | - Patrick M McCarthy
- 64 Broadsmith St, Scullin, ACT, 2614, Australia Unaffilaited Canberra Australia
| | - Claude Roux
- 390 chemin des Vignes vieilles, 84120 Mirabeau, France Unaffilaited Mirabeau France
| | - Max Mallen-Cooper
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, NSW, 2052, Australia University of New South Wales Sydney Sydney Australia
| | - Gintaras Kantvilas
- 64 Broadsmith St, Scullin, ACT, 2614, Australia Unaffilaited Canberra Australia
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104
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The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2019; 16:331-345. [PMID: 30824884 DOI: 10.1038/s41575-019-0121-2] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The gut microbiota is a dense and diverse ecosystem that is involved in many physiological functions as well as in disease pathogenesis. It is dominated by bacteria, which have been extensively studied in the past 15 years; however, other microorganisms, such as fungi, phages, archaea and protists, are also present in the gut microbiota. Exploration of the fungal component, namely, the mycobiota, is at an early stage, and several specific technical challenges are associated with mycobiota analysis. The number of fungi in the lower gastrointestinal tract is far lower than that of bacteria, but fungal cells are much larger and much more complex than bacterial cells. In addition, a role of the mycobiota in disease, notably in IBD, is indicated by both descriptive data in humans and mechanistic data in mice. Interactions between bacteria and fungi within the gut, their functional roles and their interplay with the host and its immune system are fascinating areas that researchers are just beginning to investigate. In this Review, we discuss the newest data on the gut mycobiota and explore both the technical aspects of its study and its role in health and gastrointestinal diseases.
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105
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Hernández-Restrepo M, Bezerra J, Tan Y, Wiederhold N, Crous P, Guarro J, Gené J. Re-evaluation of Mycoleptodiscus species and morphologically similar fungi. PERSOONIA 2019; 42:205-227. [PMID: 31551619 PMCID: PMC6712544 DOI: 10.3767/persoonia.2019.42.08] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/07/2019] [Indexed: 11/25/2022]
Abstract
Mycoleptodiscus includes plant pathogens, animal opportunists, saprobic and endophytic fungi. The present study presents the first molecular phylogeny and revision of the genus based on four loci, including ITS, LSU, rpb2, and tef1. An extensive collection of Mycoleptodiscus cultures, including ex-type strains from the CBS, IMI, MUCL, BRIP, clinical isolates from the USA, and fresh isolates from Brazil and Spain, was studied morphologically and phylogenetically to resolve their taxonomy. The study showed that Mycoleptodiscus sensu lato is polyphyletic. Phylogenetic analysis places Mycoleptodiscus in Muyocopronales (Dothideomycetes), together with Arxiella, Leptodiscella, Muyocopron, Neocochlearomyces, and Paramycoleptodiscus. Mycoleptodiscus terrestris, the type species, and M. sphaericus are reduced to synonyms, and one new species is introduced, M. suttonii. Mycoleptodiscus atromaculans, M. coloratus, M. freycinetiae, M. geniculatus, M. indicus, M. lateralis (including M. unilateralis and M. variabilis as its synonyms) and M. taiwanensis belong to Muyocopron (Muyocopronales, Dothideomycetes), and M. affinis, and M. lunatus to Omnidemptus (Magnaporthales, Sordariomycetes). Based on phylogenetic analyses we propose Muyocopron alcornii sp. nov., a fungus associated with leaf spots on Epidendrum sp. (Orchidaceae) in Australia, Muyocopron zamiae sp. nov. associated with leaf spots on Zamia (Zamiaceae) in the USA, and Omnidemptus graminis sp. nov. isolated from a grass (Poaceae) in Spain. Furthermore, Neomycoleptodiscus venezuelense gen. & sp. nov. is introduced for a genus similar to Mycoleptodiscus in Muyocopronaceae.
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Affiliation(s)
- M. Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - J.D.P. Bezerra
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP: 50670-901, Recife, PE, Brazil
| | - Y.P. Tan
- Queensland Plant Pathology Herbarium (BRIP), Department of Agriculture and Fisheries, Ecosciences Precinct, 41 Boggo Road, Dutton Park, Queensland, Australia 4102
| | - N. Wiederhold
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
| | - J. Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili and IISPV, C.P. 43201 Reus, Tarragona, Spain
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili and IISPV, C.P. 43201 Reus, Tarragona, Spain
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106
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Hofstetter V, Buyck B, Eyssartier G, Schnee S, Gindro K. The unbearable lightness of sequenced-based identification. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00428-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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107
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Pinto-Figueroa EA, Seddon E, Yashiro E, Buri A, Niculita-Hirzel H, van der Meer JR, Guisan A. Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities. Front Microbiol 2019; 10:656. [PMID: 31019495 PMCID: PMC6458284 DOI: 10.3389/fmicb.2019.00656] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/15/2019] [Indexed: 12/31/2022] Open
Abstract
Archaeorhizomycetes, a widespread fungal class with a dominant presence in many soil environments, contains cryptic filamentous species forming plant-root associations whose role in terrestrial ecosystems remains unclear. Here, we apply a correlative approach to identify the abiotic and biotic environmental variables shaping the distribution of this fungal group. We used a DNA sequencing dataset containing Archaeorhizomycetes sequences and environmental variables from 103 sites, obtained through a random-stratified sampling in the Western Swiss Alps along a wide elevation gradient (>2,500 m). We observed that the relative abundance of Archaeorhizomycetes follows a "humped-shaped" curve. Fitted linear and quadratic generalized linear models revealed that both climatic (minimum temperature, precipitation sum, growing degree-days) and edaphic (carbon, hydrogen, organic carbon, aluminum oxide, and phyllosilicates) factors contribute to explaining the variation in Archaeorhizomycetes abundance. Furthermore, a network inference topology described significant co-abundance patterns between Archaeorhizomycetes and other saprotrophic and ectomycorrhizal fungal taxa. Overall, our results provide strong support to the hypothesis that Archaeorhizomycetes in this area have clear ecological requirements along wide, elevation-driven abiotic and biotic gradients. Additionally, correlations to soil redox parameters, particularly with phyllosilicates minerals, suggest Archaeorhizomycetes might be implied in biological rock weathering. Such soil taxa-environment studies along wide gradients are thus a useful complement to latitudinal field observations and culture-based approaches to uncover the ecological roles of cryptic soil organisms.
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Affiliation(s)
- Eric Alejandro Pinto-Figueroa
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Emily Seddon
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Erika Yashiro
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Hélène Niculita-Hirzel
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | | | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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108
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Arredondo-Santoyo M, Domínguez C, Heras J, Mata E, Pascual V, Vázquez-Garcidueñas MS, Vázquez-Marrufo G. Automatic characterisation of dye decolourisation in fungal strains using expert, traditional, and deep features. Soft comput 2019. [DOI: 10.1007/s00500-019-03832-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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109
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Forbes JD, Bernstein CN, Tremlett H, Van Domselaar G, Knox NC. A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease? Front Microbiol 2019; 9:3249. [PMID: 30687254 PMCID: PMC6333682 DOI: 10.3389/fmicb.2018.03249] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/14/2018] [Indexed: 02/05/2023] Open
Abstract
The human microbiome has received decades of attention from scientific and medical research communities. The human gastrointestinal tract is host to immense populations of microorganisms including bacteria, viruses, archaea, and fungi (the gut microbiota). High-throughput sequencing and computational advancements provide unprecedented ability to investigate the structure and function of microbial communities associated with the human body in health and disease. Most research to date has largely focused on elucidating the bacterial component of the human gut microbiota. Study of the gut "mycobiota," which refers to the diverse array of fungal species, is a relatively new and rapidly progressing field. Though omnipresent, the number and abundance of fungi occupying the human gut is orders of magnitude smaller than that of bacteria. Recent insights however, have suggested that the gut mycobiota may be intricately linked to health and disease. Evaluation of the gut mycobiota has shown that not only are the fungal communities altered in disease, but they also play a role in maintaining intestinal homeostasis and influencing systemic immunity. In addition, it is now widely accepted that host-fungi and bacteria-fungi associations are critical to host health. While research of the gut mycobiota in health and disease is on the rise, little research has been performed in the context of neuroimmune and neurodegenerative conditions. Gut microbiota dysbiosis (specifically bacteria and archaea) have been reported in neurological diseases such as multiple sclerosis, amyotrophic lateral sclerosis, and Alzheimer's, among others. Given the widely accepted bacteria-fungi associations and paucity of mycobiota-specific studies in neurological disease, this review discusses the potential role fungi may play in multiple sclerosis and other neurological diseases. Herein, we provide an overview of recent advances in gut mycobiome research and discuss the plausible role of both intestinal and non-intestinal fungi in the context of neuroimmune and neurodegenerative conditions.
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Affiliation(s)
- Jessica D. Forbes
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Charles N. Bernstein
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Helen Tremlett
- Centre for Brain Health and Faculty of Medicine (Neurology), University of British Columbia, Vancouver, BC, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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110
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Schön ME, Nieselt K, Garnica S. Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient. PLoS One 2018; 13:e0208493. [PMID: 30517179 PMCID: PMC6281267 DOI: 10.1371/journal.pone.0208493] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Altitudinal gradients provide valuable information about the effects of environmental variables on changes in species richness and composition as well as the distribution of below ground fungal communities. Since most knowledge in this respect has been gathered on aboveground communities, we focused our study towards the characterization of belowground fungal communities associated with two different ages of Norway spruce (Picea abies) trees along an altitudinal gradient. By sequencing the internal transcribed spacer (ITS) region on the Illumina platform, we investigated the fungal communities in a floristically and geologically relatively well explored forest on the slope of Mt. Iseler of the Bavarian Alps. From fine roots and rhizosphere of a total of 90 of Norway spruce trees from 18 plots we detected 1285 taxa, with a range of 167 to 506 (average 377) taxa per plot. Fungal taxa are distributed over 96 different orders belonging to the phyla Ascomycota, Basidiomycota, Chrytridiomycota, Glomeromycota, and Mucoromycota. Overall the Agaricales (438 taxa) and Tremellales (81 taxa) belonging to the Basidiomycota and the Hypocreales (65 spp.) and Helotiales (61 taxa) belonging to the Ascomycota represented the taxon richest orders. The evaluation of our multivariate generalized mixed models indicate that the altitude has a significant influence on the composition of the fungal communities (p < 0.003) and that tree age determines community diversity (p < 0.05). A total of 47 ecological guilds were detected, of which the ectomycorrhizal and saprophytic guilds were the most taxon-rich. Our ITS amplicon Illumina sequencing approach allowed us to characterize a high fungal community diversity that would not be possible to capture with fruiting body surveys alone. We conclude that it is an invaluable tool for diverse monitoring tasks and inventorying biodiversity, especially in the detection of microorganisms developing very ephemeral and/or inconspicuous fruiting bodies or lacking them all together. Results suggest that the altitude mainly influences the community composition, whereas fungal diversity becomes higher in mature/older trees. Finally, we demonstrate that novel techniques from bacterial microbiome analyses are also useful for studying fungal diversity and community structure in a DNA metabarcoding approach, but that incomplete reference sequence databases so far limit effective identification.
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Affiliation(s)
- Max E. Schön
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Tübingen, Germany
- University of Tübingen, Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Tübingen, Germany
| | - Kay Nieselt
- University of Tübingen, Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Tübingen, Germany
| | - Sigisfredo Garnica
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Tübingen, Germany
- Universidad Austral de Chile, Instituto de Bioquímica y Microbiología, Casilla, Isla Teja, Valdivia, Chile
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111
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Wu JF, Muthusamy A, Al-Ghalith GA, Knights D, Guo B, Wu B, Remmel RP, Schladt DP, Alegre ML, Oetting WS, Jacobson PA, Israni AK. Urinary microbiome associated with chronic allograft dysfunction in kidney transplant recipients. Clin Transplant 2018; 32:e13436. [PMID: 30372560 PMCID: PMC6984979 DOI: 10.1111/ctr.13436] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/14/2018] [Accepted: 10/21/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND We performed a study to identify differences in the urinary microbiome associated with chronic allograft dysfunction (CAD) and compared the urinary microbiome of male and female transplant recipients with CAD. METHODS This case-control study enrolled 67 patients within the Deterioration of Kidney Allograft Function (DeKAF) Genomics cohort at two transplant centers. CAD was defined as a greater than 25% rise in serum creatinine relative to a 3 month post-transplant baseline. Urine samples from patients with and without CAD were analyzed using 16S V4 bacterial ribosomal DNA sequences. RESULTS Corynebacterium was more prevalent in female and male patients with CAD compared to non-CAD female patients (P = 0.0005). A total 21 distinct Operational Taxonomic Unit (OTUs) were identified as significantly different when comparing CAD and non-CAD patients using Kruskal-Wallis (P < 0.01). A subset analysis of female patients with CAD compared to non-CAD females identified similar differentially abundant OTUs, including the genera Corynebacterium and Staphylococcus (Kruskal-Wallis; P = 0.01; P = 0.004, respectively). Male CAD vs female CAD analysis showed greater abundance of phylum Proteobacteria in males. CONCLUSION There were differences in the urinary microbiome when comparing female and male CAD patients with their female non-CAD counterparts and these differences persisted in the subset analysis limited to female patients only.
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Affiliation(s)
- Jennifer F. Wu
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
| | | | | | - Dan Knights
- Department of Computer Science and Biotechnology Institute, University of Minnesota, Minneapolis, MN
| | - Bin Guo
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Rory P. Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN
| | | | - Maria-Luisa Alegre
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Ajay K. Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
- Hennepin Healthcare Research Institute, Minneapolis, MN
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112
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113
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Bates ST, Miller AN, the Macrofungi Collections and Microfungi Collections Consor . The protochecklist of North American nonlichenized Fungi. Mycologia 2018. [DOI: 10.1080/00275514.2018.1515410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Scott T. Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, Indiana 46391
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, Illinois 61820
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Andrew C, Diez J, James TY, Kauserud H. Fungarium specimens: a largely untapped source in global change biology and beyond. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170392. [PMID: 30455210 PMCID: PMC6282084 DOI: 10.1098/rstb.2017.0392] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 11/12/2022] Open
Abstract
For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Carrie Andrew
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Jeffrey Diez
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
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Vaz ABM, Fonseca PLC, Badotti F, Skaltsas D, Tomé LMR, Silva AC, Cunha MC, Soares MA, Santos VL, Oliveira G, Chaverri P, Góes-Neto A. A multiscale study of fungal endophyte communities of the foliar endosphere of native rubber trees in Eastern Amazon. Sci Rep 2018; 8:16151. [PMID: 30385829 PMCID: PMC6212449 DOI: 10.1038/s41598-018-34619-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/17/2018] [Indexed: 12/18/2022] Open
Abstract
Hevea brasiliensis is a native hyperdiverse tree species in the Amazon basin with great economic importance since it produces the highest quality natural rubber. H. brasiliensis, in its natural habitat, may harbor fungal endophytes that help defend against phytopathogenic fungi. In this work, we investigated the fungal endophytic communities in two pristine areas in Eastern Amazon (Anavilhanas National Park - ANP and Caxiuanã National Forest - CNF) at different spatial scales: regional, local, individual (tree), and intra-individual (leaflet). Using a culture-based approach, 210 fungal endophytes were isolated from 240 sampling units and assigned to 46 distinct MOTUs based on sequencing of the nrITS DNA. The community compositions of the endophytomes are different at both regional and local scales, dominated by very few taxa and highly skewed toward rare taxa, with many endophytes infrequently isolated across hosts in sampled space. Colletotrichum sp. 1, a probably latent pathogen, was the most abundant endophytic putative species and was obtained from all individual host trees in both study areas. Although the second most abundant putative species differed between the two collection sites, Clonostachys sp. 1 and Trichoderma sp. 1, they are phylogenetically related (Hypocreales) mycoparasites. Thus, they probably exhibit the same ecological function in the foliar endosphere of rubber tree as antagonists of its fungal pathogens.
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Affiliation(s)
- Aline B M Vaz
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Faculdade de Minas (FAMINAS), Belo Horizonte, MG, 31744-007, Brazil
| | - Paula L C Fonseca
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30480-000, Brazil
| | | | - Luiz M R Tomé
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Allefi C Silva
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Mayara C Cunha
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Marco A Soares
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Vera L Santos
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | | | - Priscilla Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Aristóteles Góes-Neto
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
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Angebault C, Ghozlane A, Volant S, Botterel F, d’Enfert C, Bougnoux ME. Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols. PLoS One 2018; 13:e0201174. [PMID: 30074988 PMCID: PMC6075747 DOI: 10.1371/journal.pone.0201174] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background The human intestinal microbiota contains a vast community of microorganisms increasingly studied using high-throughput DNA sequencing. Standardized protocols for storage and DNA extraction from fecal samples have been established mostly for bacterial microbiota analysis. Here, we investigated the impact of storage and DNA extraction on bacterial and fungal community structures detected concomitantly. Methods Fecal samples from healthy adults were stored at -80°C as such or diluted in RNAlater® and subjected to 2 extraction protocols with mechanical lysis: the Powersoil® MoBio kit or the International Human Microbiota Standard (IHMS) Protocol Q. Libraries of the 12 samples targeting the V3-V4 16S and the ITS1 regions were prepared using Metabiote® (Genoscreen) and sequenced on GS-FLX-454. Sequencing data were analysed using SHAMAN (http://shaman.pasteur.fr/). The bacterial and fungal microbiota were compared in terms of diversity and relative abundance. Results We obtained 171869 and 199089 quality-controlled reads for 16S and ITS, respectively. All 16S reads were assigned to 41 bacterial genera; only 52% of ITS reads were assigned to 40 fungal genera/section. Rarefaction curves were satisfactory in 3/3 and 2/3 subjects for 16S and ITS, respectively. PCoA showed important inter-individual variability of intestinal microbiota largely overweighing the effect of storage or extraction. Storage in RNAlater® impacted (downward trend) the relative abundances of 7/41 bacterial and 6/40 fungal taxa, while extraction impacted randomly 18/41 bacterial taxa and 1/40 fungal taxon. Conclusion Our results showed that RNAlater® moderately impacts bacterial or fungal community structures, while extraction significantly influences the bacterial composition. For combined bacterial and fungal intestinal microbiota analysis, immediate sample freezing should be preferred when feasible, but storage in RNAlater® remains an option under unfavourable conditions or for concomitant metatranscriptomic analysis; and extraction should rely on protocols validated for bacterial analysis, such as IHMS Protocol Q, and including a powerful mechanical lysis, essential for fungal extraction.
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Affiliation(s)
- Cécile Angebault
- Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
- Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
- Unité de Parasitologie-Mycologie, Département de Virologie, Bactériologie-Hygiène, Mycologie-Parasitologie, Unité transversale du traitement des infections (VBHMP–UT2I), DHU-VIC, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA Dynamyc 7380 UPEC, ENVA, Faculté de Médecine de Créteil, Créteil
| | - Amine Ghozlane
- Institut Pasteur, Bioinformatics and Biostatistics Hub—C3BI—USR 3756 IP CNRS, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Bioinformatics and Biostatistics Hub—C3BI—USR 3756 IP CNRS, Paris, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Virologie, Bactériologie-Hygiène, Mycologie-Parasitologie, Unité transversale du traitement des infections (VBHMP–UT2I), DHU-VIC, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA Dynamyc 7380 UPEC, ENVA, Faculté de Médecine de Créteil, Créteil
| | - Christophe d’Enfert
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, Département Mycologie, Paris, France
| | - Marie-Elisabeth Bougnoux
- Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
- Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, Département Mycologie, Paris, France
- * E-mail: ,
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Guevara MF, Mátyás B, Ordoñez ME. Xylariales: First results of mycological exploration in the Sangay and Llanganates National Parks, Ecuador. F1000Res 2018; 7:222. [PMID: 30057751 PMCID: PMC6051188 DOI: 10.12688/f1000research.13623.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 11/23/2022] Open
Abstract
Fungal samples were collected in the Sangay (SP) and Llanganates (LP) National Parks in Ecuador. Sequences of the internal transcribed spacer regions (ITS1-5.8S-ITS2) of the ribosomal DNA of the samples were analyzed.Taxonomic identification of fungi of the order Xylariales was done through phylogenetic analysis using a Maximun Likelihood method. All analyzed collections presented here belong to the genus Xylaria, of these eight belong to PL and two to SP. Four samples were not identified at the species level, suggesting it could be a new species. This data contributes with base information on the biodiversity of the Parks, necessary to design and implement measures for the conservation of fungi in Ecuador.
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Affiliation(s)
- María-Fernanda Guevara
- Biotechnology of Natural Resources, Universidad Politécnica Salesiana, Quito, 170525, Ecuador.,Environmental Research Group, Secondary Metabolites and Animal Biotechnology NUNKUY-WAKAN, Universidad Politécnica Salesiana, Quito, 170525, Ecuador
| | - Bence Mátyás
- Grupo de Investigación Mentoria y Gestión del Cambio, Universidad Politécnica Salesiana, Cuenca, 010102, Ecuador.,Grupo de Investigación Ambiental para el Desarrollo Sustentable- GIADES, Universidad Politécnica Salesiana, Quito, Ecuador
| | - María-Eugenia Ordoñez
- School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, 170143, Ecuador
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Yodphaka S, Boonpragob K, Lumbsch HT, Kraichak E. Evaluation of six regions for their potential as DNA barcodes in epiphyllous liverworts from Thailand. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01174. [PMID: 30214837 PMCID: PMC6110246 DOI: 10.1002/aps3.1174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/10/2018] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY Studies on the diversity of epiphyllous bryophytes have been limited because of minute and incomplete specimens and a lack of taxonomic expertise. The recent development of the DNA barcoding approach has allowed taxon identification and species discovery of many obscure groups of organisms. METHODS With DNA extractions from 99 samples of 16 species, we compared the efficiencies of six DNA markers (rbcL, matK, trnL-F, psbA, ITS1, and ITS2) in their ability to amplify, using a standard set of primers, as well as their discriminatory power, using distance-based and tree-based approaches with nucleotide data. RESULTS The amplification success was relatively high (70-90%) with all of the markers, except for matK, which yielded no success. The barcoding gap, as calculated from the difference between inter- and intraspecific genetic distances, was the highest in ITS2, whereas the highest numbers of monophyletic groups were found with ITS2 and rbcL. DISCUSSION rbcL should be used as a main barcoding marker with the addition of ITS2 for epiphyllous species. The development of DNA barcoding as a tool for quantifying species diversity will provide a rapid and reliable identification tool for epiphyllous bryophytes.
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Affiliation(s)
- Sorrasak Yodphaka
- Department of BotanyFaculty of ScienceKasetsart UniversityChatuchakBangkok10900,Thailand
| | - Kansri Boonpragob
- Department of BiologyFaculty of ScienceRamkamheang UniversityBangkapiBangkok10240Thailand
| | | | - Ekaphan Kraichak
- Department of BotanyFaculty of ScienceKasetsart UniversityChatuchakBangkok10900,Thailand
- Science and EducationField Museum of Natural HistoryChicagoIllinois60640USA
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Ariyawansa HA, Phillips AJL, Chuang WY, Tsai I. Tzeananiaceae, a new pleosporalean family associated with Ophiocordycepsmacroacicularis fruiting bodies in Taiwan. MycoKeys 2018:1-17. [PMID: 30100794 PMCID: PMC6072833 DOI: 10.3897/mycokeys.37.27265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/13/2018] [Indexed: 12/03/2022] Open
Abstract
The order Pleosporales comprises a miscellaneous group of fungi and is considered to be the largest order of the class Dothideomycetes. The circumscription of Pleosporales has undergone numerous changes in recent years due to the addition of large numbers of families reported from various habitats and with a large amount of morphological variation. Many asexual genera have been reported in Pleosporales and can be either hyphomycetes or coelomycetes. Phoma-like taxa are common and have been shown to be polyphyletic within the order and allied with several sexual genera. During the exploration of biodiversity of pleosporalean fungi in Taiwan, a fungal strain was isolated from mycelium growing on the fruiting body of an Ophiocordyceps species. Fruiting structures that developed on PDA were morphologically similar to Phoma and its relatives in having pycnidial conidiomata with hyaline conidia. The fungus is characterised by holoblastic, cylindrical, aseptate conidiogenous cells and cylindrical, hyaline, aseptate, guttulated, thin-walled conidia. Phylogenetic analysis based on six genes, ITS, LSU, rpb2, SSU, tef1 and tub2, produced a phylogenetic tree with the newly generated sequences grouping in a distinct clade separate from all of the known families. Therefore, a new pleosporalean family Tzeananiaceae is established to accommodate the monotypic genus Tzeanania and the species T.taiwanensis in Pleosporales, Dothideomycetes. The Ophiocordyceps species was identified as O.macroacicularis and this is a new record in Taiwan.
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Affiliation(s)
- Hiran A Ariyawansa
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taiwan National Taiwan University Taipei Taiwan
| | - Alan J L Phillips
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Campo Grande, 1749-016 Lisbon, Portugal Universidade de Lisboa Lisbon Portugal
| | - Wei-Yu Chuang
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taiwan National Taiwan University Taipei Taiwan
| | - Ichen Tsai
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taiwan National Taiwan University Taipei Taiwan
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DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists? Foods 2018; 7:foods7060087. [PMID: 29890621 PMCID: PMC6025134 DOI: 10.3390/foods7060087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Although significant progress has been made in our understanding of fungal diversity, identification based on phenotype can be difficult, even for trained experts. Fungi typically have a cryptic nature and can have a similar appearance to distantly related species. Moreover, the appearance of industrially processed mushrooms complicates species identification, as they are often sold sliced and dried. Here we present a small-scale citizen science project, wherein the participants generated and analyzed DNA sequences from fruiting bodies of dried and fresh fungi that were sold for commercial use in New York City supermarkets. We report positive outcomes and the limitations of a youth citizen scientist, aiming to identify dried mushrooms, using established DNA barcoding protocols and exclusively open-access data analysis tools for species identification. Our results indicate that the single-locus nuclear ribosomal internal transcribed spacer (ITS) DNA barcoding approach allowed for identification of only a subset of all of the samples at the species level, although the generated high-quality DNA barcodes were submitted to three different databases. Our results highlight the need for a curated, centralized, and open access ITS reference database that allows rapid third-party annotations for the benefit of both traditional research as well as the emerging citizen science community.
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121
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Lücking R, Kirk PM, Hawksworth DL. Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names. IMA Fungus 2018; 9:185-198. [PMID: 30018879 PMCID: PMC6048568 DOI: 10.5598/imafungus.2018.09.01.12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195 Berlin, Germany
| | - Paul M. Kirk
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Biodiversity Informatics & Spatial Analysis, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - David L. Hawksworth
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Jilin Agricultural University, Chanchung, Jilin province, 130118 China
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122
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Tsang CC, Tang JY, Lau SK, Woo PC. Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future. Comput Struct Biotechnol J 2018; 16:197-210. [PMID: 30002790 PMCID: PMC6039702 DOI: 10.1016/j.csbj.2018.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/12/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and computational technologies, different approaches have been adopted for the taxonomy of Aspergillus, Penicillium and Talaromyces; for example, from traditional morphotyping, phenotyping to chemotyping (e.g. lipotyping, proteotypingand metabolotyping) and then mitogenotyping and/or phylotyping. Since different taxonomic approaches focus on different sets of characters of the organisms, various classification and identification schemes would result. In view of this, the consolidated species concept, which takes into account different types of characters, is recently accepted for taxonomic purposes and, together with the lately implemented 'One Fungus - One Name' policy, is expected to bring a more stable taxonomy for Aspergillus, Penicillium and Talaromyces, which could facilitate their evolutionary studies. The most significant taxonomic change for the three genera was the transfer of Penicillium subgenus Biverticillium to Talaromyces (e.g. the medically important thermally dimorphic 'P. marneffei' endemic in Southeast Asia is now named T. marneffei), leaving both Penicillium and Talaromyces as monophyletic genera. Several distantly related Aspergillus-like fungi were also segregated from Aspergillus, making this genus, containing members of both sexual and asexual morphs, monophyletic as well. In the current omics era, application of various state-of-the-art omics technologies is likely to provide comprehensive information on the evolution of Aspergillus, Penicillium and Talaromyces and a stable taxonomy will hopefully be achieved.
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Affiliation(s)
- Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - James Y.M. Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Susanna K.P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Patrick C.Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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Palmer JM, Jusino MA, Banik MT, Lindner DL. Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data. PeerJ 2018; 6:e4925. [PMID: 29868296 PMCID: PMC5978393 DOI: 10.7717/peerj.4925] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer (ITS) amplicons, we created two ITS spike-in control mock communities composed of cloned DNA in plasmids: a biological mock community, consisting of ITS sequences from fungal taxa, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that: (1) a non-biological synthetic control (e.g., SynMock) is the best solution for parameterizing bioinformatics pipelines, (2) pre-clustering steps for variable length amplicons are critically important, (3) a major source of bias is attributed to the initial polymerase chain reaction (PCR) and thus HTAS read abundances are typically not representative of starting values. We developed AMPtk, a versatile software solution equipped to deal with variable length amplicons and quality filter HTAS data based on spike-in controls. While we describe herein a non-biological SynMock community for ITS sequences, the concept and AMPtk software can be widely applied to any HTAS dataset to improve data quality.
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Affiliation(s)
- Jonathan M. Palmer
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
| | - Michelle A. Jusino
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
| | - Mark T. Banik
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
| | - Daniel L. Lindner
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
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Colabella C, Corte L, Roscini L, Bassetti M, Tascini C, Mellor JC, Meyer W, Robert V, Vu D, Cardinali G. NGS barcode sequencing in taxonomy and diagnostics, an application in " Candida" pathogenic yeasts with a metagenomic perspective. IMA Fungus 2018; 9:91-105. [PMID: 30018874 PMCID: PMC6048569 DOI: 10.5598/imafungus.2018.09.01.07] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 05/10/2018] [Indexed: 11/29/2022] Open
Abstract
Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.
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Affiliation(s)
- Claudia Colabella
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Laura Corte
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Luca Roscini
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Matteo Bassetti
- Infectious Diseases Division, Santa Maria Misericordia University Hospital, Udine, 33100, Italy
| | - Carlo Tascini
- Infectious Diseases Division, Cotugno Hospital Napoli, 80131, Italy
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Institute for Medical Research, Sydney, NSW 2006, Australia
| | - Vincent Robert
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, 3508 CT, Utrecht, Netherlands
| | - Duong Vu
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, 3508 CT, Utrecht, Netherlands
| | - Gianluigi Cardinali
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy.,CEMIN Research Centre of Excellence, University of Perugia, Borgo 20 Giugno 74, 06121, Italy
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125
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New Ceratocystis species associated with rapid death of Metrosideros polymorpha in Hawai'i. Persoonia - Molecular Phylogeny and Evolution of Fungi 2018; 40:154-181. [PMID: 30505000 PMCID: PMC6146641 DOI: 10.3767/persoonia.2018.40.07] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/10/2018] [Indexed: 12/02/2022]
Abstract
The native ‘ōhi’a lehua (Metrosideros polymorpha) has cultural, biological and ecological significance to Hawai’i, but it is seriously threatened by a disease commonly referred to as rapid ‘ōhi’a death (ROD). Preliminary investigations showed that a Ceratocystis species similar to C. fimbriata s.lat. was the cause of the disease. In this study, we used a combination of the phylogenetic, morphological and biological species concepts, as well as pathogenicity tests and microsatellite analyses, to characterise isolates collected from diseased ‘ōhi’a trees across Hawai’i Island. Two distinct lineages, representing new species of Ceratocystis, were evident based on multigene phylogenetic analyses. These are described here as C. lukuohia and C. huliohia. Ceratocystis lukuohia forms part of the Latin American clade (LAC) and was most closely associated with isolates from Syngonium and Xanthosoma from the Caribbean and elsewhere, including Hawai’i, and C. platani, which is native to eastern USA. Ceratocystis huliohia resides in the Asian-Australian clade (AAC) and is most closely related to C. uchidae, C. changhui and C. cercfabiensis, which are thought to be native to Asia. Morphology and interfertility tests support the delineation of these two new species and pathogenicity tests show that both species are aggressive pathogens on seedlings of M. polymorpha. Characterisation of isolates using microsatellite markers suggest that both species are clonal and likely represent recently-introduced strains. Intensive research is underway to develop rapid screening protocols for early detection of the pathogens and management strategies in an attempt to prevent the spread of the pathogens to the other islands of Hawai’i, which are currently disease free.
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126
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Abstract
In recent years, the gut microbiota has been considered as a full-fledged actor of the gut-brain axis, making it possible to take a new step in understanding the pathophysiology of both neurological and psychiatric diseases. However, most of the studies have been devoted to gut bacterial microbiota, forgetting the non-negligible fungal flora. In this review, we expose how the role of the fungal component in the microbiota-gut-brain axis is legitimate, through its interactions with both the host, especially with the immune system, and the gut bacteria. We also discuss published data that already attest to a role of the mycobiome in the microbiota-gut-brain axis, and the impact of fungi on clinical and therapeutic research.
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127
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Liu Y, Erséus C. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida). Ecol Evol 2017; 7:10421-10439. [PMID: 29238565 PMCID: PMC5723599 DOI: 10.1002/ece3.3212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022] Open
Abstract
Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.
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Affiliation(s)
- Yingkui Liu
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
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128
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Colabella C, Corte L, Roscini L, Shapaval V, Kohler A, Tafintseva V, Tascini C, Cardinali G. Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species. PLoS One 2017; 12:e0188104. [PMID: 29206226 PMCID: PMC5714347 DOI: 10.1371/journal.pone.0188104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023] Open
Abstract
The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance, molecular taxonomy, FT-IR technique and chemo-metrics, data management and data basing.
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Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Laura Corte
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Luca Roscini
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Valeria Tafintseva
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Carlo Tascini
- Azienda Ospedaliera dei Colli—Ospedale Cotugno, Napoli, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials—Department of Chemistry, Biology and Biotechnology—University of Perugia, Perugia, Italy
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129
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Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev 2017; 41:479-511. [PMID: 28430946 DOI: 10.1093/femsre/fuw047] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'mycobiome'. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
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Affiliation(s)
- Chloe E Huseyin
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
| | - Pauline D Scanlan
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
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130
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Brunner I, Frey B, Hartmann M, Zimmermann S, Graf F, Suz LM, Niskanen T, Bidartondo MI, Senn-Irlet B. Ecology of Alpine Macrofungi - Combining Historical with Recent Data. Front Microbiol 2017; 8:2066. [PMID: 29123508 PMCID: PMC5662630 DOI: 10.3389/fmicb.2017.02066] [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: 06/23/2017] [Accepted: 10/09/2017] [Indexed: 11/13/2022] Open
Abstract
Historical datasets of living communities are important because they can be used to document creeping shifts in species compositions. Such a historical data set exists for alpine fungi. From 1941 to 1953, the Swiss geologist Jules Favre visited yearly the region of the Swiss National Park and recorded the occurring fruiting bodies of fungi >1 mm (so-called “macrofungi”) in the alpine zone. Favre can be regarded as one of the pioneers of alpine fungal ecology not least because he noted location, elevation, geology, and associated plants during his numerous excursions. However, some relevant information is only available in his unpublished field-book. Overall, Favre listed 204 fungal species in 26 sampling sites, with 46 species being previously unknown. The analysis of his data revealed that the macrofungi recorded belong to two major ecological groups, either they are symbiotrophs and live in ectomycorrhizal associations with alpine plant hosts, or they are saprotrophs and decompose plant litter and soil organic matter. The most frequent fungi were members of Inocybe and Cortinarius, which form ectomycorrhizas with Dryas octopetala or the dwarf alpine Salix species. The scope of the present study was to combine Favre's historical dataset with more recent data, either with the “SwissFungi” database or with data from major studies of the French and German Alps, and with the data from novel high-throughput DNA sequencing techniques of soils from the Swiss Alps. Results of the latter application revealed, that problems associated with these new techniques are manifold and species determination remains often unclear. At this point, the fungal taxa collected by Favre and deposited as exsiccata at the “Conservatoire et Jardin Botaniques de la Ville de Genève” could be used as a reference sequence dataset for alpine fungal studies. In conclusion, it can be postulated that new improved databases are urgently necessary for the near future, particularly, with regard to investigating fungal communities from alpine regions using new techniques.
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Affiliation(s)
- Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Stephan Zimmermann
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Frank Graf
- Community Ecology, WSL Institute for Snow and Avalanche Research SLF, Davos Dorf, Switzerland
| | - Laura M Suz
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Tuula Niskanen
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Martin I Bidartondo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom.,Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Beatrice Senn-Irlet
- Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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131
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de Beer ZW, Marincowitz S, Duong TA, Wingfield MJ. Bretziella, a new genus to accommodate the oak wilt fungus, Ceratocystis fagacearum (Microascales, Ascomycota). MycoKeys 2017. [DOI: 10.3897/mycokeys.27.20657] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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132
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Zhang N, Luo J, Bhattacharya D. Advances in Fungal Phylogenomics and Their Impact on Fungal Systematics. ADVANCES IN GENETICS 2017; 100:309-328. [PMID: 29153403 DOI: 10.1016/bs.adgen.2017.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In the past decade, advances in next-generation sequencing technologies and bioinformatic pipelines for phylogenomic analysis have led to remarkable progress in fungal systematics and taxonomy. A number of long-standing questions have been addressed using comparative analysis of genome sequence data, resulting in robust multigene phylogenies. These have added to, and often surpassed traditional morphology or single-gene phylogenetic methods. In this chapter, we provide a brief history of fungal systematics and highlight some examples to demonstrate the impact of phylogenomics on this field. We conclude by discussing some of the challenges and promises in fungal biology posed by the ongoing genomics revolution.
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Affiliation(s)
- Ning Zhang
- Rutgers University, New Brunswick, NJ, United States.
| | - Jing Luo
- Rutgers University, New Brunswick, NJ, United States
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133
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Tascini C, Sozio E, Corte L, Sbrana F, Scarparo C, Ripoli A, Bertolino G, Merelli M, Tagliaferri E, Corcione A, Bassetti M, Cardinali G, Menichetti F. The role of biofilm forming on mortality in patients with candidemia: a study derived from real world data. Infect Dis (Lond) 2017; 50:214-219. [PMID: 28988525 DOI: 10.1080/23744235.2017.1384956] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evaluation of the role on patient mortality exerted by biofilm forming (BF) Candida strains, by using predictive clinical data. METHODS Eighty-nine strains isolated from Candida bloodstream infection, occurring in two Italian University Hospitals, were employed in this study. A random forest (RF) model was built with a procedure of iterative selection of the risk factors potentially able to predict the probability of death. The similarity between patient conditions and Bayesian clustering was calculated in order to evaluate the role of predictors in the stratification of the death risk. RESULTS Three different groups of patients with different probability of death were obtained with a RF approach: Group 1 (mortality in 33.3% of cases), Group 2 (death in 50% of cases), and Group 3 (mortality in 76.9% of cases). The comparison between these three groups showed that BF correlated well with increased mortality in patients, admitted for medical diagnosis, with high APACHE II score and treated with azoles. Early treatment within 24 h between candidemia diagnosis and the beginning of antifungal therapy was associated with the lowest of BF rate and mortality. CONCLUSIONS BF by Candida spp. seems to be clinically associated with increased mortality especially in medical patients with higher Apache II score or treated with azoles.
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Affiliation(s)
- Carlo Tascini
- a First Division of Infectious Diseases , Cotugno Hospital, Azienda Ospedaliera dei Colli , Napoli , Italy
| | - Emanuela Sozio
- b Unit of Emergency Medicine , Nuovo Santa Chiara University Hospital, Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| | - Laura Corte
- c Department of Pharmaceutical Sciences-Microbiology , University of Perugia , Perugia , Italy.,d CEMIN (Centre of Excellence on Nanostructured Innovative Materials), Department of Chemistry, Biology and Biotechnology , University of Perugia , Perugia , Italy
| | | | - Claudio Scarparo
- f Unit of Microbiology , Santa Maria Misericordia University Hospital , Udine , Italy
| | - Andrea Ripoli
- d CEMIN (Centre of Excellence on Nanostructured Innovative Materials), Department of Chemistry, Biology and Biotechnology , University of Perugia , Perugia , Italy
| | - Giacomo Bertolino
- g Department of Pharmaceutical Sciences-Medicine management , Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| | - Maria Merelli
- h Division of Infectious Diseases , Santa Maria Misericordia University Hospital , Udine , Italy
| | - Enrico Tagliaferri
- i Infectious Diseases Clinic , Nuovo Santa Chiara University Hospital, Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| | - Antonio Corcione
- j Department of Intensive Care , Monaldi Hospital, Azienda Ospedaliera dei Colli , Napoli , Italy
| | - Matteo Bassetti
- h Division of Infectious Diseases , Santa Maria Misericordia University Hospital , Udine , Italy
| | - Gianluigi Cardinali
- c Department of Pharmaceutical Sciences-Microbiology , University of Perugia , Perugia , Italy.,d CEMIN (Centre of Excellence on Nanostructured Innovative Materials), Department of Chemistry, Biology and Biotechnology , University of Perugia , Perugia , Italy
| | - Francesco Menichetti
- i Infectious Diseases Clinic , Nuovo Santa Chiara University Hospital, Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
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134
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Cardinali G, Corte L, Robert V. Next Generation Sequencing: problems and opportunities for next generation studies of microbial communities in food and food industry. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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135
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136
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Nilsson RH, Sánchez-García M, Ryberg MK, Abarenkov K, Wurzbacher C, Kristiansson E. Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 2017. [DOI: 10.3897/mycokeys.26.14591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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137
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Van den Wyngaert S, Seto K, Rojas-Jimenez K, Kagami M, Grossart HP. A New Parasitic Chytrid, Staurastromyces oculus (Rhizophydiales, Staurastromycetaceae fam. nov.), Infecting the Freshwater Desmid Staurastrum sp. Protist 2017; 168:392-407. [DOI: 10.1016/j.protis.2017.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
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138
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Molecular identification of cestodes and nematodes by cox1 gene real-time PCR and sequencing. Diagn Microbiol Infect Dis 2017; 89:185-190. [PMID: 28865743 DOI: 10.1016/j.diagmicrobio.2017.07.012] [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] [Received: 02/13/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/22/2022]
Abstract
Unlike bacteria and fungi, identification of helminths by gene sequencing is not well-standardized. No "pan-cestode" or "pan-nematode" PCR primers are available. In this study, we designed 2 pairs of PCR primers for amplifying the cox1 genes of cestodes and nematodes respectively and validated their usefulness for real-time PCR and sequencing identification using clinical samples with cestodes and nematodes collected from a variety of animals and human in 7 countries in Asia, Europe and Africa. The detection limits of the cox1 real-time PCR assays for cestodes and nematodes were 10 copies/reaction of extracted DNA, corresponding to CT values of 33 and 31 respectively. Real-time PCR using the 2 pairs of primers and probes showed positive results for all 20 clinical samples of cestodes and nematodes. Using phenotypic identification results as the reference standard, DNA sequencing successfully identified all the 5 cestodes and 7 nematodes with cox1 gene sequences available in GenBank, with all these names appearing as the best match of the cox1 gene sequences of the corresponding clinical samples. The percentage nucleotide identities between the cox1 gene sequences of the samples and those of the corresponding best match sequences in GenBank were 98-100%. For the remaining 5 cestodes and 3 nematodes, the corresponding cox1 gene sequences were not available in GenBank. cox1 gene sequencing is discriminative enough for accurately identifying most of the cestodes and nematodes in the present study. Further expansion of the cox1 gene sequence database will enable accurate identification of more cestodes and nematodes.
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139
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Aspergillus labruscus sp. nov., a new species of Aspergillus section Nigri discovered in Brazil. Sci Rep 2017; 7:6203. [PMID: 28740180 PMCID: PMC5524721 DOI: 10.1038/s41598-017-06589-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 11/08/2022] Open
Abstract
A novel fungal species, Aspergillus labruscus sp. nov., has been found in Brazil during an investigation of the fungal species present on the surface of grape berries (Vitis labrusca L.) for use in the production of concentrated grape juice. It seems to be associated to V. labrusca, and has never been recovered from Vitis vinifera. This new species belonging to Aspergillus subgenus Circumdati section Nigri is described here using morphological characters, extrolite profiling, partial sequence data from the BenA and CaM genes, and internal transcribed spacer sequences of ribosomal DNA. Phenotypic and molecular data enabled this novel species to be clearly distinguished from other black aspergilli. A. labruscus sp. nov. is uniseriate, has yellow mycelium, poor sporulation on CYA at 25 °C, abundant salmon to pink sclerotia and rough conidia. Neoxaline and secalonic acid D were consistently produced by isolates in this taxon. The type strain of A. labruscus sp. nov. is CCT 7800 (T) = ITAL 22.223 (T) = IBT 33586 (T).
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140
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Yeasts. Microbiol Spectr 2017; 4. [PMID: 27726781 DOI: 10.1128/microbiolspec.dmih2-0030-2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeasts are unicellular organisms that reproduce mostly by budding and less often by fission. Most medically important yeasts originate from Ascomycota or Basidiomycota. Here, we review taxonomy, epidemiology, disease spectrum, antifungal drug susceptibility patterns of medically important yeast, laboratory diagnosis, and diagnostic strategies.
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141
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Monggoot S, Popluechai S, Gentekaki E, Pripdeevech P. Fungal Endophytes: an Alternative Source for Production of Volatile Compounds from Agarwood Oil of Aquilaria subintegra. MICROBIAL ECOLOGY 2017; 74:54-61. [PMID: 28058469 DOI: 10.1007/s00248-016-0908-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Fungal endophytes are microorganisms that are well-known for producing a diverse array of secondary metabolites. Recent studies have uncovered the bioprospecting potential of several plant endophytic fungi. Here, we demonstrate the presence of highly bioactive fungal endophytic species in Aquilaria subintegra, a fragrant wood plant collected from Thailand. Thirty-three fungal endophytic strains were isolated and further identified to genus level based on morphological characteristics. These genera included Colletotrichum, Pestalotiopsis, Fusarium, Russula, Arthrinium, Diaporthe and Cladosporium. All strains were cultured on potato dextrose broth for 30 days prior to partitioning with ethyl acetate. The volatile compounds of all extracts were investigated by gas chromatography-mass spectrometry (GC-MS). Four strains-Arthrinium sp. MFLUCC16-0042, Colletotrichum sp. MFLUCC16-0047, Colletotrichum sp. MFLUCC16-0048 and Diaporthe sp. MFLUCC16-0051-produced a broad spectrum of volatile compounds, including β-agarofuran, α-agarofuran, δ-eudesmol, oxo-agarospirol, and β-dihydro agarofuran. These compounds are especially important, because they greatly resemble those originating from the host-produced agarwood oil. Our findings demonstrate the potential of endophytic fungi to produce bioactive compounds with applications in perfumery and cosmetic industries. Antioxidant activity of all extracts was also evaluated by using 2,2-diphenyl-2-picrylhydrazyl radical scavenging assays. The ethyl acetate extract of Diaporthe sp. MFLUCC16-0051 demonstrated superior antioxidant capacity, which was comparable to that of the gallic acid standard. Our results indicate that the MFLUCC16-0051 strain is a resource of natural antioxidant with potential medicinal applications.
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Affiliation(s)
- Sakon Monggoot
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Siam Popluechai
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
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142
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Mattana S, Alunni Cardinali M, Caponi S, Casagrande Pierantoni D, Corte L, Roscini L, Cardinali G, Fioretto D. High-contrast Brillouin and Raman micro-spectroscopy for simultaneous mechanical and chemical investigation of microbial biofilms. Biophys Chem 2017; 229:123-129. [PMID: 28684254 DOI: 10.1016/j.bpc.2017.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/21/2017] [Accepted: 06/21/2017] [Indexed: 12/18/2022]
Abstract
Mechanical mapping with chemical specificity of biological samples is now made possible by joint micro-Brillouin and micro-Raman measurements. In this work, thanks to the unprecedented contrast of a new tandem Fabry-Perot interferometer, we demonstrate simultaneous detection of Brillouin and Raman spectra from different Candida biofilms. Our proof-of-concept study reveals the potential of this label-free joint micro-spectroscopy technique in challenging microbiological issues. In particular, heterogeneous chemo-mechanical maps of Candida biofilms are obtained, without the need for staining or touching the sample. The correlative Raman and Brillouin investigation evidences the role of both extracellular polymeric substances and of hydration water in inducing a marked local softening of the biofilm.
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Affiliation(s)
- S Mattana
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy.
| | - M Alunni Cardinali
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - S Caponi
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - D Casagrande Pierantoni
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy
| | - L Corte
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy
| | - L Roscini
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy
| | - G Cardinali
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy; CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - D Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy; CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
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143
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Chen SCA, Meyer W, Pashley CH. Challenges in Laboratory Detection of Fungal Pathogens in the Airways of Cystic Fibrosis Patients. Mycopathologia 2017; 183:89-100. [PMID: 28589247 DOI: 10.1007/s11046-017-0150-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/20/2017] [Indexed: 12/11/2022]
Abstract
Study of the clinical significance of fungal colonization/infection in the airways of cystic fibrosis (CF) patients, especially by filamentous fungi, is challenged by the absence of standardized methodology for the detection and identification of an ever-broadening range of fungal pathogens. Culture-based methods remain the cornerstone diagnostic approaches, but current methods used in many clinical laboratories are insensitive and unstandardized, rendering comparative studies unfeasible. Guidelines for standardized processing of respiratory specimens and for their culture are urgently needed and should include recommendations for specific processing procedures, inoculum density, culture media, incubation temperature and duration of culture. Molecular techniques to detect fungi directly from clinical specimens include panfungal PCR assays, multiplex or pathogen-directed assays, real-time PCR, isothermal methods and probe-based assays. In general, these are used to complement culture. Fungal identification by DNA sequencing methods is often required to identify cultured isolates, but matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is increasingly used as an alternative to DNA sequencing. Genotyping of isolates is undertaken to investigate relatedness between isolates, to pinpoint the infection source and to study the population structure. Methods range from PCR fingerprinting and amplified fragment length polymorphism analysis, to short tandem repeat typing, multilocus sequencing typing (MLST) and whole genome sequencing (WGS). MLST is the current preferred method, whilst WGS offers best case resolution but currently is understudied.
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Affiliation(s)
- Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, 3rd Level ICPMR Building, Westmead, NSW, 2145, Australia.
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia.
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Catherine H Pashley
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, LE1 9HN, UK
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144
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Crous P, Wingfield M, Burgess T, Hardy G, Barber P, Alvarado P, Barnes C, Buchanan P, Heykoop M, Moreno G, Thangavel R, van der Spuy S, Barili A, Barrett S, Cacciola S, Cano-Lira J, Crane C, Decock C, Gibertoni T, Guarro J, Guevara-Suarez M, Hubka V, Kolařík M, Lira C, Ordoñez M, Padamsee M, Ryvarden L, Soares A, Stchigel A, Sutton D, Vizzini A, Weir B, Acharya K, Aloi F, Baseia I, Blanchette R, Bordallo J, Bratek Z, Butler T, Cano-Canals J, Carlavilla J, Chander J, Cheewangkoon R, Cruz R, da Silva M, Dutta A, Ercole E, Escobio V, Esteve-Raventós F, Flores J, Gené J, Góis J, Haines L, Held B, Jung MH, Hosaka K, Jung T, Jurjević Ž, Kautman V, Kautmanova I, Kiyashko A, Kozanek M, Kubátová A, Lafourcade M, La Spada F, Latha K, Madrid H, Malysheva E, Manimohan P, Manjón J, Martín M, Mata M, Merényi Z, Morte A, Nagy I, Normand AC, Paloi S, Pattison N, Pawłowska J, Pereira O, Petterson M, Picillo B, Raj K, Roberts A, Rodríguez A, Rodríguez-Campo F, Romański M, Ruszkiewicz-Michalska M, Scanu B, Schena L, Semelbauer M, Sharma R, Shouche Y, Silva V, Staniaszek-Kik M, Stielow J, Tapia C, Taylor P, Toome-Heller M, Vabeikhokhei J, van Diepeningen A, Van Hoa N, M. VT, Wiederhold N, Wrzosek M, Zothanzama J, Groenewald J. Fungal Planet description sheets: 558-624. PERSOONIA 2017; 38:240-384. [PMID: 29151634 PMCID: PMC5645186 DOI: 10.3767/003158517x698941] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 05/01/2017] [Indexed: 01/20/2023]
Abstract
Novel species of fungi described in this study include those from various countries as follows: Australia: Banksiophoma australiensis (incl. Banksiophoma gen. nov.) on Banksia coccinea, Davidiellomycesaustraliensis (incl. Davidiellomyces gen. nov.) on Cyperaceae, Didymocyrtis banksiae on Banksia sessilis var. cygnorum, Disculoides calophyllae on Corymbia calophylla, Harknessia banksiae on Banksia sessilis, Harknessia banksiae-repens on Banksia repens, Harknessia banksiigena on Banksia sessilis var. cygnorum, Harknessia communis on Podocarpus sp., Harknessia platyphyllae on Eucalyptus platyphylla, Myrtacremonium eucalypti (incl. Myrtacremonium gen. nov.) on Eucalyptus globulus, Myrtapenidiella balenae on Eucalyptus sp., Myrtapenidiella eucalyptigena on Eucalyptus sp., Myrtapenidiella pleurocarpae on Eucalyptuspleurocarpa, Paraconiothyrium hakeae on Hakea sp., Paraphaeosphaeria xanthorrhoeae on Xanthorrhoea sp., Parateratosphaeria stirlingiae on Stirlingia sp., Perthomyces podocarpi (incl. Perthomyces gen. nov.) on Podocarpus sp., Readeriella ellipsoidea on Eucalyptus sp., Rosellinia australiensis on Banksia grandis, Tiarosporella corymbiae on Corymbia calophylla, Verrucoconiothyriumeucalyptigenum on Eucalyptus sp., Zasmidium commune on Xanthorrhoea sp., and Zasmidium podocarpi on Podocarpus sp. Brazil: Cyathus aurantogriseocarpus on decaying wood, Perenniporia brasiliensis on decayed wood, Perenniporia paraguyanensis on decayed wood, and Pseudocercospora leandrae-fragilis on Leandrafragilis.Chile: Phialocephala cladophialophoroides on human toe nail. Costa Rica: Psathyrella striatoannulata from soil. Czech Republic: Myotisia cremea (incl. Myotisia gen. nov.) on bat droppings. Ecuador: Humidicutis dictiocephala from soil, Hygrocybe macrosiparia from soil, Hygrocybe sangayensis from soil, and Polycephalomyces onorei on stem of Etlingera sp. France: Westerdykella centenaria from soil. Hungary: Tuber magentipunctatum from soil. India: Ganoderma mizoramense on decaying wood, Hodophilus indicus from soil, Keratinophyton turgidum in soil, and Russula arunii on Pterigota alata.Italy: Rhodocybe matesina from soil. Malaysia: Apoharknessia eucalyptorum, Harknessia malayensis, Harknessia pellitae, and Peyronellaea eucalypti on Eucalyptus pellita, Lectera capsici on Capsicum annuum, and Wallrothiella gmelinae on Gmelina arborea.Morocco: Neocordana musigena on Musa sp. New Zealand: Candida rongomai-pounamu on agaric mushroom surface, Candida vespimorsuum on cup fungus surface, Cylindrocladiella vitis on Vitis vinifera, Foliocryphia eucalyptorum on Eucalyptus sp., Ramularia vacciniicola on Vaccinium sp., and Rhodotorula ngohengohe on bird feather surface. Poland: Tolypocladium fumosum on a caterpillar case of unidentified Lepidoptera.Russia: Pholiotina longistipitata among moss. Spain: Coprinopsis pseudomarcescibilis from soil, Eremiomyces innocentii from soil, Gyroporus pseudocyanescens in humus, Inocybe parvicystis in humus, and Penicillium parvofructum from soil. Unknown origin: Paraphoma rhaphiolepidis on Rhaphiolepsis indica.USA: Acidiella americana from wall of a cooling tower, Neodactylaria obpyriformis (incl. Neodactylaria gen. nov.) from human bronchoalveolar lavage, and Saksenaea loutrophoriformis from human eye. Vietnam: Phytophthora mekongensis from Citrus grandis, and Phytophthora prodigiosa from Citrus grandis. Morphological and culture characteristics along with DNA barcodes are provided.
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Affiliation(s)
- P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - M.J. Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - T.I. Burgess
- Centre for Phytophthora Science and Management, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - G.E.St.J. Hardy
- Centre for Phytophthora Science and Management, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - P.A. Barber
- ArborCarbon, P.O. Box 1065, Willagee Central, WA 6156, Australia; 1 City Farm Place, East Perth, Western Australia, 6004 Australia
| | - P. Alvarado
- ALVALAB, C/ La Rochela nº 47, E-39012 Santander, Spain
| | - C.W. Barnes
- Instituto Nacional de Investigaciones Agropecuarias, Estación Experimental Santa Catalina, Panamericana Sur Km1, Sector Cutuglahua, Pichincha, Ecuador
| | - P.K. Buchanan
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
| | - M. Heykoop
- Departamento de Ciencias de la Vida (Área de Botánica), Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - G. Moreno
- Departamento de Ciencias de la Vida (Área de Botánica), Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - R. Thangavel
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - S. van der Spuy
- Macleans College, 2 Macleans Rd, Bucklands Beach, Auckland 2014, New Zealand
| | - A. Barili
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076 y Roca, Quito, Ecuador
| | - S. Barrett
- Department of Parks and Wildlife Albany District, 120 Albany Highway, Albany, WA 6330, Australia
| | - S.O. Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy
| | - J.F. Cano-Lira
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - C. Crane
- Department of Parks and Wildlife, Vegetation Health Service, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983, Australia
| | - C. Decock
- Mycothèque de l’Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute – Microbiology (ELIM), Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348, Louvain-la-Neuve, Belgium
| | - T.B. Gibertoni
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Recife, Brazil
| | - J. Guarro
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - M. Guevara-Suarez
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - C.R.S. Lira
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Recife, Brazil
| | - M.E. Ordoñez
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076 y Roca, Quito, Ecuador
| | - M. Padamsee
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
| | - L. Ryvarden
- University of Oslo, Institute of Biological Sciences, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - A.M. Soares
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Recife, Brazil
| | - A.M. Stchigel
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - D.A. Sutton
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy; Institute for Sustainable Plant Protection (IPSP)-CNR, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | - B.S. Weir
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
| | - K. Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - F. Aloi
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy
| | - I.G. Baseia
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - R.A. Blanchette
- University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - J.J. Bordallo
- Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Z. Bratek
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, Pázmány Péter lane 1/C, Budapest H-1117, Hungary
| | - T. Butler
- Te Kura Kaupapa Māori o Kaikohe, 20 Hongi Street, Kaikohe 0405, New Zealand
| | - J. Cano-Canals
- Te Kura Kaupapa Māori o Kaikohe, 20 Hongi Street, Kaikohe 0405, New Zealand
| | - J.R. Carlavilla
- Departamento de Ciencias de la Vida (Área de Botánica), Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - J. Chander
- Department of Microbiology, Government Medical College Hospital, 32B, Sector 32, Chandigarh, 160030, India
| | - R. Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - R.H.S.F. Cruz
- Programa de Pós-graduação em Sistemática e Evolução, Dept. Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, 59078-970, Brazil
| | - M. da Silva
- Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - A.K. Dutta
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - E. Ercole
- Department of Life Sciences and Systems Biology, University of Turin, I-10125 Turin, Italy
| | - V. Escobio
- Sociedad Micológica de Gran Canaria, Apartado 609, 35080 Las Palmas de Gran Canaria, Spain
| | - F. Esteve-Raventós
- Departamento de Ciencias de la Vida (Área de Botánica), Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - J.A. Flores
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076 y Roca, Quito, Ecuador
| | - J. Gené
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - J.S. Góis
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - L. Haines
- Te Kura Kaupapa Māori o Kaikohe, 20 Hongi Street, Kaikohe 0405, New Zealand
| | - B.W. Held
- University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - M. Horta Jung
- Phytophthora Research Center, Mendel University, Zemedelska 1, 613 00 Brno, Czech Republic; Phytophthora Research and Consultancy, Am Rain 9, 83131 Nußdorf, Germany
| | - K. Hosaka
- Department of Botany, National Museum of Nature and Science-TNS, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - T. Jung
- Phytophthora Research Center, Mendel University, Zemedelska 1, 613 00 Brno, Czech Republic; Phytophthora Research and Consultancy, Am Rain 9, 83131 Nußdorf, Germany
| | - Ž. Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077, USA
| | | | - I. Kautmanova
- Slovak National Museum-Natural History Museum, Vajanskeho nab. 2, P.O. Box 13, 81006 Bratislava, Slovakia
| | - A.A. Kiyashko
- Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - M. Kozanek
- Scientica, Ltd., Hybesova 33, 83106 Bratislava, Slovakia
| | - A. Kubátová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
| | - M. Lafourcade
- Laboratorio Clínico, Clínica Santa María, Santiago, Chile
| | - F. La Spada
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy
| | - K.P.D. Latha
- Department of Botany, University of Calicut, Kerala, 673 635, India
| | - H. Madrid
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor de Chile, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - E.F. Malysheva
- Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - P. Manimohan
- Department of Botany, University of Calicut, Kerala, 673 635, India
| | - J.L. Manjón
- Departamento de Ciencias de la Vida (Área de Botánica), Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - M.P. Martín
- Departamento de Micología, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - M. Mata
- Escuela de Biología, Universidad de Costa Rica, Sede Central, San Pedro de Montes Oca. San José, Costa Rica
| | - Z. Merényi
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, Pázmány Péter lane 1/C, Budapest H-1117, Hungary
| | - A. Morte
- Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - I. Nagy
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, Pázmány Péter lane 1/C, Budapest H-1117, Hungary
| | - A.-C. Normand
- Département de Parasitologie/Mycologie La Timone, Marseille, France
| | - S. Paloi
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - N. Pattison
- Rongomai School, 20 Rongomai Rd, Otara, Auckland 2023, New Zealand
| | - J. Pawłowska
- Department of Molecular Phylogenetics and Evolution, University of Warsaw, Żwirki and Wigury 101, PL-02-089 Warsaw, Poland
| | - O.L. Pereira
- Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - M.E. Petterson
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
| | - B. Picillo
- Via Roma 139, I-81017 Sant’ Angelo d’ Alife (CE), Italy
| | - K.N.A. Raj
- Department of Botany, University of Calicut, Kerala, 673 635, India
| | - A. Roberts
- Karamu High School, Windsor Ave, Parkvale, Hastings 4122, New Zealand
| | - A. Rodríguez
- Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | | | - M. Romański
- Wigry National Park, Krzywe 82, PL-16-402 Suwałki, Poland
| | | | - B. Scanu
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - L. Schena
- Dipartimento di Agraria, Mediterranean University of Reggio Calabria, Feo di Vito, 89122 Reggio Calabria, Italy
| | - M. Semelbauer
- Institute of Zoology, Slovak Academy of Sciences, Dubravska cesta 9, 84506 Bratislava, Slovakia
| | - R. Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex SP Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Y.S. Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex SP Pune University Campus, Ganeshkhind, Pune 411007, India
| | - V. Silva
- Escuela de Tecnología Médica, Facultad de Ciencias, Universidad Mayor de Chile, Santiago, Chile
| | - M. Staniaszek-Kik
- Department of Geobotany and Plant Ecology, University of Łódź, Banacha 12/16, PL-90-237 Łódź, Poland
| | - J.B. Stielow
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - C. Tapia
- Laboratorio de Micología Médica, Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Australia
| | - M. Toome-Heller
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | | | - A.D. van Diepeningen
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - N. Van Hoa
- Southern Horticultural Research Institute, My Tho, Tien Giang, Vietnam
| | - Van Tri M.
- Southern Horticultural Research Institute, My Tho, Tien Giang, Vietnam
| | - N.P. Wiederhold
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - M. Wrzosek
- Department of Molecular Phylogenetics and Evolution, University of Warsaw, Żwirki and Wigury 101, PL-02-089 Warsaw, Poland
| | | | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
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145
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Zhao G, Yin G, Inamdar AA, Luo J, Zhang N, Yang I, Buckley B, Bennett JW. Volatile organic compounds emitted by filamentous fungi isolated from flooded homes after Hurricane Sandy show toxicity in a Drosophila bioassay. INDOOR AIR 2017; 27:518-528. [PMID: 27748984 DOI: 10.1111/ina.12350] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Superstorm Sandy provided an opportunity to study filamentous fungi (molds) associated with winter storm damage. We collected 36 morphologically distinct fungal isolates from flooded buildings. By combining traditional morphological and cultural characters with an analysis of ITS sequences (the fungal DNA barcode), we identified 24 fungal species that belong to eight genera: Penicillium (11 species), Fusarium (four species), Aspergillus (three species), Trichoderma (two species), and one species each of Metarhizium, Mucor, Pestalotiopsis, and Umbelopsis. Then, we used a Drosophila larval assay to assess possible toxicity of volatile organic compounds (VOCs) emitted by these molds. When cultured in a shared atmosphere with growing cultures of molds isolated after Hurricane Sandy, larval toxicity ranged from 15 to 80%. VOCs from Aspergillus niger 129B were the most toxic yielding 80% mortality to Drosophila after 12 days. The VOCs from Trichoderma longibrachiatum 117, Mucor racemosus 138a, and Metarhizium anisopliae 124 were relatively non-toxigenic. A preliminary analysis of VOCs was conducted using solid-phase microextraction-gas chromatography-mass spectrometry from two of the most toxic, two of the least toxic, and two species of intermediate toxicity. The more toxic molds produced higher concentrations of 1-octen-3-ol, 3-octanone, 3-octanol, 2-octen-1-ol, and 2-nonanone; while the less toxic molds produced more 3-methyl-1-butanol and 2-methyl-1-propanol, or an overall lower amount of volatiles. Our data support the hypothesis that at certain concentrations, some VOCs emitted by indoor molds are toxigenic.
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Affiliation(s)
- G Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - G Yin
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - A A Inamdar
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - J Luo
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - N Zhang
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - I Yang
- Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - B Buckley
- Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - J W Bennett
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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146
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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147
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Yin G, Zhang Y, Pennerman KK, Wu G, Hua SST, Yu J, Jurick WM, Guo A, Bennett JW. Characterization of Blue Mold Penicillium Species Isolated from Stored Fruits Using Multiple Highly Conserved Loci. J Fungi (Basel) 2017; 3:E12. [PMID: 29371531 PMCID: PMC5715957 DOI: 10.3390/jof3010012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 02/04/2023] Open
Abstract
Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locations, and years. Based on morphological and cultural characteristics and partial amplification of the β-tubulin locus, the isolates were provisionally identified as several different species of Penicillium. These isolates were investigated further using a suite of molecular DNA markers and compared to sequences of the ex-type for cognate species in GenBank, and were identified as P. expansum (3 isolates), P. solitum (3 isolates), P. carneum (1 isolate), and P. paneum (1 isolate). Three of the markers we used (ITS, internal transcribed spacer rDNA sequence; benA, β-tubulin; CaM, calmodulin) were suitable for distinguishing most of our isolates from one another at the species level. In contrast, we were unable to amplify RPB2 sequences from four of the isolates. Comparison of our sequences with cognate sequences in GenBank from isolates with the same species names did not always give coherent data, reinforcing earlier studies that have shown large intraspecific variability in many Penicillium species, as well as possible errors in some sequence data deposited in GenBank.
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Affiliation(s)
- Guohua Yin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 5711001, China.
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Yuliang Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 5711001, China.
| | - Kayla K Pennerman
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Guangxi Wu
- Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA.
| | - Sui Sheng T Hua
- U.S. Department of Agriculture, Agricultural Research Service , Western Regional Research Center, Albany, CA 94710, USA.
| | - Jiujiang Yu
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Agricultural Research Center, Beltsville, MD 20705, USA.
| | - Wayne M Jurick
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Agricultural Research Center, Beltsville, MD 20705, USA.
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 5711001, China.
| | - Joan W Bennett
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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148
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Marin-Felix Y, Groenewald J, Cai L, Chen Q, Marincowitz S, Barnes I, Bensch K, Braun U, Camporesi E, Damm U, de Beer Z, Dissanayake A, Edwards J, Giraldo A, Hernández-Restrepo M, Hyde K, Jayawardena R, Lombard L, Luangsa-ard J, McTaggart A, Rossman A, Sandoval-Denis M, Shen M, Shivas R, Tan Y, van der Linde E, Wingfield M, Wood A, Zhang J, Zhang Y, Crous P. Genera of phytopathogenic fungi: GOPHY 1. Stud Mycol 2017; 86:99-216. [PMID: 28663602 PMCID: PMC5486355 DOI: 10.1016/j.simyco.2017.04.002] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genera of Phytopathogenic Fungi (GOPHY) is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.
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Affiliation(s)
- Y. Marin-Felix
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - S. Marincowitz
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - I. Barnes
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Botanische Staatssammlung München, Menzinger Straße 67, D-80638 München, Germany
| | - U. Braun
- Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik und Botanischer Garten, Herbarium, Neuwerk 21, D-06099 Halle (Saale), Germany
| | - E. Camporesi
- A.M.B. Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forlì, Italy
- A.M.B. Circolo Micologico “Giovanni Carini”, C.P. 314, Brescia, Italy
- Società per gli Studi Naturalistici della Romagna, C.P. 144, Bagnacavallo (RA), Italy
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Z.W. de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Dissanayake
- Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - J. Edwards
- AgriBio Centre for AgriBiosciences, Department of Economic Development, Jobs, Transport and Resources, 5 Ring Road, LaTrobe University, Bundoora, Victoria 3083, Australia
| | - A. Giraldo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - M. Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - K.D. Hyde
- Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - R.S. Jayawardena
- Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - J. Luangsa-ard
- Microbe Interaction and Ecology Laboratory, Biodiversity and Biotechnological Resource Research Unit (BBR), BIOTEC, NSTDA 113 Thailand Science Park Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - A.R. McTaggart
- Department of Plant and Soil Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A.Y. Rossman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - M. Shen
- Institute of Microbiology, P.O. Box 61, Beijing Forestry University, Beijing 100083, PR China
| | - R.G. Shivas
- Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern Queensland, Toowoomba 4350, Queensland, Australia
| | - Y.P. Tan
- Department of Agriculture & Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CT Utrecht, The Netherlands
| | - E.J. van der Linde
- ARC – Plant Protection Research Institute, Biosystematics Division – Mycology, P. Bag X134, Queenswood 0121, South Africa
| | - M.J. Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A.R. Wood
- ARC – Plant Protection Research Institute, P. Bag X5017, Stellenbosch 7599, South Africa
| | - J.Q. Zhang
- Institute of Microbiology, P.O. Box 61, Beijing Forestry University, Beijing 100083, PR China
| | - Y. Zhang
- Institute of Microbiology, P.O. Box 61, Beijing Forestry University, Beijing 100083, PR China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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149
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Motooka D, Fujimoto K, Tanaka R, Yaguchi T, Gotoh K, Maeda Y, Furuta Y, Kurakawa T, Goto N, Yasunaga T, Narazaki M, Kumanogoh A, Horii T, Iida T, Takeda K, Nakamura S. Fungal ITS1 Deep-Sequencing Strategies to Reconstruct the Composition of a 26-Species Community and Evaluation of the Gut Mycobiota of Healthy Japanese Individuals. Front Microbiol 2017; 8:238. [PMID: 28261190 PMCID: PMC5309391 DOI: 10.3389/fmicb.2017.00238] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/03/2017] [Indexed: 12/18/2022] Open
Abstract
The study of mycobiota remains relatively unexplored due to the lack of sufficient available reference strains and databases compared to those of bacterial microbiome studies. Deep sequencing of Internal Transcribed Spacer (ITS) regions is the de facto standard for fungal diversity analysis. However, results are often biased because of the wide variety of sequence lengths in the ITS regions and the complexity of high-throughput sequencing (HTS) technologies. In this study, a curated ITS database, ntF-ITS1, was constructed. This database can be utilized for the taxonomic assignment of fungal community members. We evaluated the efficacy of strategies for mycobiome analysis by using this database and characterizing a mock fungal community consisting of 26 species representing 15 genera using ITS1 sequencing with three HTS platforms: Illumina MiSeq (MiSeq), Ion Torrent Personal Genome Machine (IonPGM), and Pacific Biosciences (PacBio). Our evaluation demonstrated that PacBio's circular consensus sequencing with greater than 8 full-passes most accurately reconstructed the composition of the mock community. Using this strategy for deep-sequencing analysis of the gut mycobiota in healthy Japanese individuals revealed two major mycobiota types: a single-species type composed of Candida albicans or Saccharomyces cerevisiae and a multi-species type. In this study, we proposed the best possible processing strategies for the three sequencing platforms, of which, the PacBio platform allowed for the most accurate estimation of the fungal community. The database and methodology described here provide critical tools for the emerging field of mycobiome studies.
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Affiliation(s)
- Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University Suita, Japan
| | - Kosuke Fujimoto
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka UniversitySuita, Japan; Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka UniversitySuita, Japan
| | - Reiko Tanaka
- Division of Bio-resources, Medical Mycology Research Center, Chiba University Chiba, Japan
| | - Takashi Yaguchi
- Division of Bio-resources, Medical Mycology Research Center, Chiba University Chiba, Japan
| | - Kazuyoshi Gotoh
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka UniversitySuita, Japan; Department of Bacteriology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
| | - Yuichi Maeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka UniversitySuita, Japan; Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka UniversitySuita, Japan
| | - Yoki Furuta
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University Suita, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University Suita, Japan
| | - Naohisa Goto
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University Suita, Japan
| | - Teruo Yasunaga
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University Suita, Japan
| | - Masashi Narazaki
- Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University Suita, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University Suita, Japan
| | - Toshihiro Horii
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University Suita, Japan
| | - Tetsuya Iida
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University Suita, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University Suita, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University Suita, Japan
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150
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Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform. J Clin Microbiol 2017; 55:1011-1024. [PMID: 28179406 DOI: 10.1128/jcm.02084-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform.
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