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Visagie CM, Meijer M, Kraak B, Groenewald M, Houbraken J, Theelen B, Vorst Y, Boekhout T. Blastobotrys nigripullensis, a new yeast species isolated from a fungal outbreak on an ancient Roman shipwreck in the Netherlands. Antonie Van Leeuwenhoek 2024; 117:22. [PMID: 38217778 DOI: 10.1007/s10482-023-01898-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/08/2023] [Indexed: 01/15/2024]
Abstract
A new species of the yeast genus Blastobotrys was discovered on ancient ship timbers in the Netherlands. The species had developed on the wood of a river barge dating to the Roman period. The growth occurred after the preservative polyethylene glycol (PEG 4000) was washed out of some of the timbers due to an undetected leak in the storage unit. Mycological analysis of various timber samples revealed the presence of Microascus melanosporus (predominant), Microascus paisii, a member of the Acremonium chrysogenum-clade, and a new Blastrobotrys species. The new species produced sporothrix-like conidiophores with clavate blastoconidia (3-7 × 1-3.5 μm) and was found to be osmotolerant, capable of growth on low water activity media like malt yeast 50% glucose agar (MY50G). In this article we formally describe and introduce Blastrobotrys nigripullensis (CBS 17879 T) based on its morphology, physiology and phylogenetic placement.
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Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin Meijer
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | - Bart Kraak
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | | | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute (WI), Utrecht, The Netherlands
| | - Yardeni Vorst
- Museumpark Archeon, Restoration Project: Operation Zwammerdam ships, Alphen aan den Rijn, The Netherlands
| | - Teun Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia.
- Retired from Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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Visagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast 2023; 40:7-31. [PMID: 36168284 PMCID: PMC10108157 DOI: 10.1002/yea.3816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 01/18/2023] Open
Abstract
A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.
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Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Neriman Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Keith A Seifert
- Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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Rush RE, Dannemiller KC, Cochran SJ, Haines SR, Acosta L, Divjan A, Rundle AG, Miller RL, Perzanowski MS, Croston TL, Green BJ. Vishniacozyma victoriae (syn. Cryptococcus victoriae) in the homes of asthmatic and non-asthmatic children in New York City. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2022; 32:48-59. [PMID: 34091598 PMCID: PMC10032026 DOI: 10.1038/s41370-021-00342-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/19/2021] [Accepted: 04/29/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Indoor environments contain a broad diversity of non-pathogenic Basidiomycota yeasts, but their role in exacerbating adverse health effects has remained unclear. OBJECTIVE To understand the role of Vishniacozyma victoriae exposure and its impact on human health. METHODS A qPCR assay was developed to detect and quantify an abundant indoor yeast species, Vishniacozyma victoriae (syn. Cryptococcus victoriae), from homes participating in the New York City Neighborhood Asthma and Allergy Study (NAAS). We evaluated the associations between V. victoriae, housing characteristics, and asthma relevant health endpoints. RESULTS V. victoriae was quantified in 236 of the 256 bedroom floor dust samples ranging from less than 300-45,918 cell equivalents/mg of dust. Higher concentrations of V. victoriae were significantly associated with carpeted bedroom floors (P = 0.044), mean specific humidity (P = 0.004), winter (P < 0.0001) and spring (P = 0.001) seasons, and the presence of dog (P = 0.010) and dog allergen Can f 1 (P = 0.027). V. victoriae concentrations were lower in homes of children with asthma vs. without asthma (P = 0.027), an association observed only among the non-seroatopic children.
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Affiliation(s)
- Rachael E Rush
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV, USA
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Karen C Dannemiller
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, Ohio State University, Columbus, OH, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
| | - Samuel J Cochran
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, Ohio State University, Columbus, OH, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
- Environmental Sciences Graduate Program, Ohio State University, Columbus, OH, USA
| | - Sarah R Haines
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, Ohio State University, Columbus, OH, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
- Environmental Sciences Graduate Program, Ohio State University, Columbus, OH, USA
| | - Luis Acosta
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Adnan Divjan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Andrew G Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rachel L Miller
- Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Matthew S Perzanowski
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Tara L Croston
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Brett J Green
- Office of the Director, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.
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Olgun NS, Morris AM, Stefaniak AB, Bowers LN, Knepp AK, Duling MG, Mercer RR, Kashon ML, Fedan JS, Leonard SS. Biological effects of inhaled hydraulic fracturing sand dust. III. Cytotoxicity and pro-inflammatory responses in cultured murine macrophage cells. Toxicol Appl Pharmacol 2020; 408:115281. [PMID: 33065155 PMCID: PMC7952011 DOI: 10.1016/j.taap.2020.115281] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/16/2022]
Abstract
Cultured murine macrophages (RAW 264.7) were used to investigate the effects of fracking sand dust (FSD) for its pro-inflammatory activity, in order to gain insight into the potential toxicity to workers associated with inhalation of FSD during hydraulic fracturing. While the role of respirable crystalline silica in the development of silicosis is well documented, nothing is known about the toxicity of inhaled FSD. The FSD (FSD 8) used in these studies was from an unconventional gas well drilling site. FSD 8was prepared as a 10 mg/ml stock solution in sterile PBS, vortexed for 15 s, and allowed to sit at room temperature for 30 min before applying the suspension to RAW 264.7cells. Compared to PBS controls, cellular viability was significantly decreased after a 24 h exposure to FSD. Intracellular reactive oxygen species (ROS) production and the production of IL-6, TNFα, and endothelin-1 (ET-1) were up-regulated as a result of the exposure, whereas the hydroxyl radical (.OH) was only detected in an acellular system. Immunofluorescent staining of cells against TNFα revealed that FSD 8 caused cellular blebbing, and engulfment of FSD 8 by macrophages was observed with enhanced dark-field microscopy. The observed changes in cellular viability, cellular morphology, free radical generation and cytokine production all confirm that FSD 8 is cytotoxic to RAW 264.7 cells and warrants future studies into the specific pathways and mechanisms by which these toxicities occur.
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Affiliation(s)
- Nicole S Olgun
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America.
| | - Anna M Morris
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Aleksandr B Stefaniak
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Lauren N Bowers
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Alycia K Knepp
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Matthew G Duling
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Robert R Mercer
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Michael L Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Jeffrey S Fedan
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
| | - Stephen S Leonard
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, United States of America
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Microbial Interaction with Clay Minerals and Its Environmental and Biotechnological Implications. MINERALS 2020. [DOI: 10.3390/min10100861] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clay minerals are very common in nature and highly reactive minerals which are typical products of the weathering of the most abundant silicate minerals on the planet. Over recent decades there has been growing appreciation that the prime involvement of clay minerals in the geochemical cycling of elements and pedosphere genesis should take into account the biogeochemical activity of microorganisms. Microbial intimate interaction with clay minerals, that has taken place on Earth’s surface in a geological time-scale, represents a complex co-evolving system which is challenging to comprehend because of fragmented information and requires coordinated efforts from both clay scientists and microbiologists. This review covers some important aspects of the interactions of clay minerals with microorganisms at the different levels of complexity, starting from organic molecules, individual and aggregated microbial cells, fungal and bacterial symbioses with photosynthetic organisms, pedosphere, up to environmental and biotechnological implications. The review attempts to systematize our current general understanding of the processes of biogeochemical transformation of clay minerals by microorganisms. This paper also highlights some microbiological and biotechnological perspectives of the practical application of clay minerals–microbes interactions not only in microbial bioremediation and biodegradation of pollutants but also in areas related to agronomy and human and animal health.
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Kiss L, Vaghefi N, Bransgrove K, Dearnaley JDW, Takamatsu S, Tan YP, Marston C, Liu SY, Jin DN, Adorada DL, Bailey J, Cabrera de Álvarez MG, Daly A, Dirchwolf PM, Jones L, Nguyen TD, Edwards J, Ho W, Kelly L, Mintoff SJL, Morrison J, Németh MZ, Perkins S, Shivas RG, Smith R, Stuart K, Southwell R, Turaganivalu U, Váczy KZ, Blommestein AV, Wright D, Young A, Braun U. Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery of Salmonomyces as a New Lineage of the Erysiphales. Front Microbiol 2020; 11:1571. [PMID: 32765452 PMCID: PMC7378747 DOI: 10.3389/fmicb.2020.01571] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent.
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Affiliation(s)
- Levente Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Niloofar Vaghefi
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Kaylene Bransgrove
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, QLD, Australia
| | - John D. W. Dearnaley
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Susumu Takamatsu
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- Laboratory of Plant Pathology, Faculty of Bioresources, Mie University, Tsu, Japan
| | - Yu Pei Tan
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, QLD, Australia
| | - Craig Marston
- Science and Surveillance Group, Department of Agriculture, Water and the Environment, Brisbane, QLD, Australia
| | - Shu-Yan Liu
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Dan-Ni Jin
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Dante L. Adorada
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Jordan Bailey
- Plant Pathology & Mycology Herbarium, New South Wales Department of Primary Industries, Orange, NSW, Australia
| | | | - Andrew Daly
- Plant Health Diagnostic Service, New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Pamela Maia Dirchwolf
- Department of Plant Protection, Faculty of Agricultural Science, National University of the Northeast, Corrientes, Argentina
| | - Lynne Jones
- Science and Surveillance Group, Department of Agriculture, Water and the Environment, Brisbane, QLD, Australia
| | | | - Jacqueline Edwards
- Agriculture Victoria Research, Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Wellcome Ho
- New Zealand Ministry for Primary Industries, Auckland, New Zealand
| | - Lisa Kelly
- Department of Agriculture and Fisheries, Queensland Government, Toowoomba, QLD, Australia
| | - Sharl J. L. Mintoff
- Department of Primary Industry and Resources, Northern Territory Government, Darwin, NT, Australia
| | - Jennifer Morrison
- Science and Surveillance Group, Department of Agriculture, Water and the Environment, Brisbane, QLD, Australia
| | - Márk Z. Németh
- Plant Protection Institute, Centre for Agricultural Research, Budapest, Hungary
| | - Sandy Perkins
- Science and Surveillance Group, Department of Agriculture, Water and the Environment, Brisbane, QLD, Australia
| | - Roger G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, QLD, Australia
| | - Reannon Smith
- Agriculture Victoria Research, Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Kara Stuart
- Ecosciences Precinct, Department of Agriculture and Fisheries, Dutton Park, QLD, Australia
| | - Ronald Southwell
- Science and Surveillance Group, Department of Agriculture, Water and the Environment, Sydney, NSW, Australia
| | | | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly University, Eger, Hungary
| | - Annie Van Blommestein
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Dominie Wright
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Anthony Young
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Uwe Braun
- Herbarium, Department of Geobotany and Botanical Garden, Institute for Biology, Martin Luther University, Halle (Saale), Germany
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Timm CM, Loomis K, Stone W, Mehoke T, Brensinger B, Pellicore M, Staniczenko PP, Charles C, Nayak S, Karig DK. Isolation and characterization of diverse microbial representatives from the human skin microbiome. MICROBIOME 2020; 8:58. [PMID: 32321582 PMCID: PMC7178971 DOI: 10.1186/s40168-020-00831-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/18/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND The skin micro-environment varies across the body, but all sites are host to microorganisms that can impact skin health. Some of these organisms are true commensals which colonize a unique niche on the skin, while open exposure of the skin to the environment also results in the transient presence of diverse microbes with unknown influences on skin health. Culture-based studies of skin microbiota suggest that skin microbes can affect skin properties, immune responses, pathogen growth, and wound healing. RESULTS In this work, we greatly expanded the diversity of available commensal organisms by collecting > 800 organisms from 3 body sites of 17 individuals. Our collection includes > 30 bacterial genera and 14 fungal genera, with Staphylococcus and Micrococcus as the most prevalent isolates. We characterized a subset of skin isolates for the utilization of carbon compounds found on the skin surface. We observed that members of the skin microbiota have the capacity to metabolize amino acids, steroids, lipids, and sugars, as well as compounds originating from personal care products. CONCLUSIONS This collection is a resource that will support skin microbiome research with the potential for discovery of novel small molecules, development of novel therapeutics, and insight into the metabolic activities of the skin microbiota. We believe this unique resource will inform skin microbiome management to benefit skin health. Video abstract.
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Affiliation(s)
- Collin M. Timm
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
| | - Kristin Loomis
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
| | - William Stone
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
| | - Thomas Mehoke
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
| | - Bryan Brensinger
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
| | - Matthew Pellicore
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
| | | | - Curtisha Charles
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Seema Nayak
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - David K. Karig
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD USA
- Department of Bioengineering, Clemson University, Clemson, SC USA
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Abstract
Atopy and fungi have a long associative history. Fungal spores were among the first substances to which humans were noted to be sensitized. Humans contact fungal spores in the outdoor, indoor, and occupational environments. As organisms, fungi have their own kingdom and are found in all environmental niches on earth. Currently, fungal exposure in the indoor environment especially related to wet housing conditions is of particular concern. Sensitization rates to fungi typically exceed 5% of the general public with higher rates among the atopic population. Alternaria is the best studied of the allergic fungi; however, cross sensitization to multiple fungi is well documented. Recent advances in understanding mechanisms of the innate immune system are beginning to explain why the fungal atopy relationship is unique and why fungal sensitivity seems to extend to many non-atopic individuals. Evidence has been accumulated that indicates fungal allergen exposure can be via intact spores as well as spore and mycelial fragments. Germinating spores produce a different and often increased allergen picture. Much evidence has been developed through animal studies that extends the mechanisms surrounding long-term low-level fungal exposure. However, it should be emphasized that the presence of fungi in the air does not necessarily equate with illness. Indeed, in the absence of an atopic individual and/or a significant immune response against fungi, there is little evidence suggesting pathology. Allergists frequently deal with patients who have concerns about indoor fungal exposure and respiratory disease in those patients with an allergic response.
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Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S. Microbiome as an Immunological Modifier. Methods Mol Biol 2020; 2055:595-638. [PMID: 31502171 PMCID: PMC8276114 DOI: 10.1007/978-1-4939-9773-2_27] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.
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Affiliation(s)
- Manoj Kumar
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Selvasankar Murugesan
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Marie Vetizou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souhaila Al Khodor
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar.
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Lemons AR, Croston TL, Goldsmith WT, Barnes MA, Jaderson MA, Park JH, McKinney W, Beezhold DH, Green BJ. Cultivation and aerosolization of Stachybotrys chartarum for modeling pulmonary inhalation exposure. Inhal Toxicol 2019; 31:446-456. [PMID: 31874574 DOI: 10.1080/08958378.2019.1705939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Objective: Stachybotrys chartarum is a hydrophilic fungal species commonly found as a contaminant in water-damaged building materials. Although several studies have suggested that S. chartarum exposure elicits a variety of adverse health effects, the ability to characterize the pulmonary immune responses to exposure is limited by delivery methods that do not replicate environmental exposure. This study aimed to develop a method of S. chartarum aerosolization to better model inhalation exposures. Materials and methods: An acoustical generator system (AGS) was previously developed and utilized to aerosolize and deliver fungal spores to mice housed in a multi-animal nose-only exposure chamber. In this study, methods for cultivating, heat-inactivating, and aerosolizing two macrocyclic trichothecene-producing strains of S. chartartum using the AGS are described. Results and discussion: In addition to conidia, acoustical generation of one strain of S. chartarum resulted in the aerosolization of fungal fragments (<2 µm aerodynamic diameter) derived from conidia, phialides, and hyphae that initially comprised 50% of the total fungal particle count but was reduced to less than 10% over the duration of aerosolization. Acoustical generation of heat-inactivated S. chartarum did not result in a similar level of fragmentation. Delivery of dry, unextracted S. chartarum using these aerosolization methods resulted in pulmonary inflammation and immune cell infiltration in mice inhaling viable, but not heat-inactivated S. chartarum. Conclusions: These methods of S. chartarum growth and aerosolization allow for the delivery of fungal bioaerosols to rodents that may better simulate natural exposure within water-damaged indoor environments.
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Affiliation(s)
- Angela R Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Tara L Croston
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - W Travis Goldsmith
- Engineering and Control Technology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Mark A Barnes
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Mukhtar A Jaderson
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ju-Hyeong Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Walter McKinney
- Engineering and Control Technology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Donald H Beezhold
- Office of the Director, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Brett J Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
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12
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Małek M, Mrowiec P, Klesiewicz K, Skiba-Kurek I, Szczepański A, Białecka J, Żak I, Bogusz B, Kędzierska J, Budak A, Karczewska E. Prevalence of human pathogens of the clade Nakaseomyces in a culture collection-the first report on Candida bracarensis in Poland. Folia Microbiol (Praha) 2018; 64:307-312. [PMID: 30361876 PMCID: PMC6529382 DOI: 10.1007/s12223-018-0655-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
Human pathogens belonging to the Nakaseomyces clade include Candida glabrata sensu stricto, Candida nivariensis and Candida bracarensis. Their highly similar phenotypic characteristics often lead to misidentification by conventional laboratory methods. Therefore, limited information on the true epidemiology of the Candida glabrata species complex is available. Due to life-threatening infections caused by these species, it is crucial to supplement this knowledge. The aim of the study was to estimate the prevalence of C. bracarensis and C. nivariensis in a culture collection of C. glabrata complex isolates. The study covered 353 isolates identified by biochemical methods as C. glabrata, collected from paediatric and adult patients hospitalised at four medical centres in Southern Poland. The multiplex PCR was used to identify the strains. Further species confirmation was performed via sequencing and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) analysis. One isolate was recognised as C. bracarensis (0.28%). To our knowledge, it is the first isolate in Poland. C. glabrata sensu stricto species has been confirmed for all the remaining isolates. No C. nivariensis was found. Our study has shown that the prevalence of C. nivariensis and C. bracarensis strains is infrequent. However, it should be emphasised that the incidence of these strains may differ locally and depend on environmental factors and the population.
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Affiliation(s)
- Marianna Małek
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688, Kraków, Poland.
| | - Paulina Mrowiec
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688, Kraków, Poland.
| | - Karolina Klesiewicz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688, Kraków, Poland
| | - Iwona Skiba-Kurek
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688, Kraków, Poland
| | - Adrian Szczepański
- Department of Microbiology, University Hospital in Kraków, Kraków, Poland
| | - Joanna Białecka
- Centre for Microbiological Research and Autovaccines, Kraków, Poland
| | - Iwona Żak
- Department of Microbiology, University Children's Hospital of Kraków, Kraków, Poland
| | - Bożena Bogusz
- Department of Microbiology, Ludwik Rydygier Memorial Hospital in Kraków, Kraków, Poland
| | - Jolanta Kędzierska
- Department of Microbiology, University Hospital in Kraków, Kraków, Poland
| | - Alicja Budak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688, Kraków, Poland
| | - Elżbieta Karczewska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688, Kraków, Poland
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Abstract
PURPOSE OF REVIEW The evolution of molecular-based methods over the last two decades has provided new approaches to identify and characterize fungal communities or "mycobiomes" at resolutions previously not possible using traditional hazard identification methods. The recent focus on fungal community assemblages within indoor environments has provided renewed insight into overlooked sources of fungal exposure. In occupational studies, internal transcribed spacer (ITS) region sequencing has recently been utilized in a variety of environments ranging from indoor office buildings to agricultural commodity and harvesting operations. RECENT FINDINGS Fungal communities identified in occupational environments have been primarily placed in the phylum Ascomycota and included classes typically identified using traditional fungal exposure methods such as the Eurotiomycetes, Dothideomycetes, Sordariomycetes, and Saccharomycetes. The phylum Basidiomycota has also been reported to be more prevalent than previously estimated and ITS region sequences have been primarily derived from the classes Agaricomycetes and Ustilaginomycetes. These studies have also resolved sequences placed in the Basidiomycota classes Tremellomycetes and Exobasidiomycetes that include environmental and endogenous yeast species. These collective datasets have shown that occupational fungal exposures include a much broader diversity of fungi than once thought. Although the clinical implications for occupational allergy are an emerging field of research, establishing the mycobiome in occupational environments will be critical for future studies to determine the complete spectrum of worker exposures to fungal bioaerosols and their impact on worker health.
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14
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Park JH, Sulyok M, Lemons AR, Green BJ, Cox-Ganser JM. Characterization of fungi in office dust: Comparing results of microbial secondary metabolites, fungal internal transcribed spacer region sequencing, viable culture and other microbial indices. INDOOR AIR 2018; 28:10.1111/ina.12470. [PMID: 29729045 PMCID: PMC6215746 DOI: 10.1111/ina.12470] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/24/2018] [Indexed: 05/26/2023]
Abstract
Recent developments in molecular and chemical methods have enabled the analysis of fungal DNA and secondary metabolites, often produced during fungal growth, in environmental samples. We compared 3 fungal analytical methods by analysing floor dust samples collected from an office building for fungi using viable culture, internal transcribed spacer (ITS) sequencing and secondary metabolites using liquid chromatography-tandem mass spectrometry. Of the 32 metabolites identified, 29 had a potential link to fungi with levels ranging from 0.04 (minimum for alternariol monomethylether) to 5700 ng/g (maximum for neoechinulin A). The number of fungal metabolites quantified per sample ranged from 8 to 16 (average = 13/sample). We identified 216 fungal operational taxonomic units (OTUs) with the number per sample ranging from 6 to 29 (average = 18/sample). We identified 37 fungal species using culture, and the number per sample ranged from 2 to 13 (average = 8/sample). Agreement in identification between ITS sequencing and culturing was weak (kappa = -0.12 to 0.27). The number of cultured fungal species poorly correlated with OTUs, which did not correlate with the number of metabolites. These suggest that using multiple measurement methods may provide an improved understanding of fungal exposures in indoor environments and that secondary metabolites may be considered as an additional source of exposure.
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Affiliation(s)
- Ju-Hyeong Park
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown WV, USA
| | - Michael Sulyok
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna, Austria
| | - Angela R. Lemons
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown WV, USA
| | - Brett J. Green
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown WV, USA
| | - Jean M. Cox-Ganser
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown WV, USA
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15
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Lemons AR, Lindsley WG, Green BJ. Collection and Extraction of Occupational Air Samples for Analysis of Fungal DNA. J Vis Exp 2018. [PMID: 29782003 DOI: 10.3791/56730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several limitations that have resulted in the exclusion of many species. Advances in the field over the last two decades have led occupational health researchers to turn to molecular-based approaches for identifying fungal hazards. These methods have resulted in the detection of many species within indoor and occupational environments that have not been detected using traditional methods. This protocol details an approach for determining fungal diversity within air samples through genomic DNA extraction, amplification, sequencing, and taxonomic identification of fungal internal transcribed spacer (ITS) regions. ITS sequencing results in the detection of many fungal species that are either not detected or difficult to identify to species level using culture or microscopy. While these methods do not provide quantitative measures of fungal burden, they offer a new approach to hazard identification and can be used to determine overall species richness and diversity within an occupational environment.
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Affiliation(s)
- Angela R Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention;
| | - William G Lindsley
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention
| | - Brett J Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention
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16
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Green BJ, Couch JR, Lemons AR, Burton NC, Victory KR, Nayak AP, Beezhold DH. Microbial hazards during harvesting and processing at an outdoor United States cannabis farm. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2018; 15:430-440. [PMID: 29370578 PMCID: PMC6314012 DOI: 10.1080/15459624.2018.1432863] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cannabis cultivation is an emerging industry within the United States. Organic dust derived in part from naturally occurring microorganisms is known to cause byssinosis in the hemp industry. In this pilot study, bacteria and fungi encountered by workers at an outdoor cannabis farm that utilized organic practices were elucidated by 16 S ribosomal RNA (rRNA) and Internal Transcribed Spacer (ITS) region sequencing, respectively. Area (n = 14) and personal air samples (n = 12) were collected during harvesting and processing activities. 16 S rRNA and ITS regions of extracted bacterial and fungal genomic DNA were amplified and sequenced using Sanger sequencing. Bacterial sequencing resolved 1,077 sequences that were clustered into 639 operational taxonomic units (OTUs) and predominantly placed in the phylum, Actinobacteria (46%). Personal air samples revealed higher bacterial and Actinobacteria diversity compared to outdoor area samples collected within the facility (p < 0.05). A high degree of dissimilarity between bacteria was identified within and between samples. Fungal sequences (n = 985) were identified and predominantly clustered in the phylum Ascomycota (53%). Of the 216 fungal OTUs elucidated, the cannabis plant pathogenic species, Botrytis cinerea, was the most prevalent and accounted for 34% of all fungal sequences. The relative abundance of B. cinerea was highest in personal air samples (59%) compared to area samples collected in the drying room (19%), greenhouse (18%), and outdoor environment (6%). There was 49% sample similarity between fungi identified within personal air samples, but higher dissimilarity coefficients were observed within and between greenhouse, drying room, and outdoor area air samples. The results of this pilot study suggest that the cannabis farm workers are potentially exposed to Actinobacteria as well as the cannabis plant pathogen, B. cinerea during harvesting, bud-stripping, and hand-trimming processes.
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Affiliation(s)
- Brett J. Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
- Corresponding author: Brett J. Green, Allergy and Clinical Immunology Branch, Health Effects Laboratory Branch, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, WV 26505,
| | - James R. Couch
- Hazard Evaluations and Technical Assistance Branch, Division of Surveillance, Hazard Evaluations and Field Studies, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, OH, USA
| | - Angela R. Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Nancy C. Burton
- Hazard Evaluations and Technical Assistance Branch, Division of Surveillance, Hazard Evaluations and Field Studies, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, OH, USA
| | - Kerton R. Victory
- Office of the Director, Emergency Preparedness and Response Office, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ajay P. Nayak
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Donald H. Beezhold
- Office of the Director, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
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17
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Coombs K, Taft D, Ward DV, Green BJ, Chew GL, Shamsaei B, Meller J, Indugula R, Reponen T. Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:212-218. [PMID: 28803198 PMCID: PMC6728913 DOI: 10.1016/j.scitotenv.2017.07.274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 05/30/2023]
Abstract
"Green" housing is designed to use low-impact materials, increase energy efficiency and improve occupant health. However, little is known about the indoor mycobiome of green homes. The current study is a subset of a multicenter study that aims to investigate the indoor environment of green homes and the respiratory health of asthmatic children. In the current study, the mycobiome in air, bed dust and floor dust was compared between green (study site) and non-green (control site), low-income homes in Cincinnati, Ohio. The samples were collected at baseline (within four months following renovation), and 12months after the baseline at the study site. Parallel sample collection was conducted in non-green control homes. Air samples were collected by PM2.5 samplers over 5-days. Bed and floor dust samples were vacuumed after the air sampling was completed. The DNA sample extracts were analyzed using ITS amplicon sequencing. Analysis indicated that there was no clear trend in the fungal communities between green and non-green homes. Instead, fungal community differences were greatest between sample types - air, bed, and floor. Microbial communities also changed substantially between sampling intervals in both green and non-green homes for all sample types, potentially indicating that there was very little stability in the mycobiomes. Research gaps remain regarding how indoor mycobiome fluctuates over time. Longer follow-up periods might elucidate the effect of green renovation on microbial load in buildings.
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Affiliation(s)
- Kanistha Coombs
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, Cincinnati, OH, USA
| | - Diana Taft
- University of California at Davis, Department of Food Science and Technology, One Shields Ave., Davis, CA, USA
| | - Doyle V Ward
- University of Massachusetts Medical School, Center for Microbiome Research, 55 N Lake Ave, Worcester, MA, USA; University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, 55 N Lake Ave North, Worcester, MA, USA
| | - Brett J Green
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Health Effects Laboratory Division, Allergy and Clinical Immunology Branch, 1095 Willowdale Road, Morgantown, WV, USA
| | - Ginger L Chew
- Centers for Disease Control and Prevention, National Center for Environmental Health, Air Pollution and Respiratory Health Branch, 4770 Buford Hwy, N.E., MS-F60 Atlanta, GA, USA
| | - Behrouz Shamsaei
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, Cincinnati, OH, USA
| | - Jaroslaw Meller
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, Cincinnati, OH, USA; Cincinnati Children's Hospital Research Foundation, Division of Biomedical Informatics, 3333 Burnett Avenue, Cincinnati, OH, USA
| | - Reshmi Indugula
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, Cincinnati, OH, USA
| | - Tiina Reponen
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, Cincinnati, OH, USA.
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18
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Humphries Z, Seifert KA, Hirooka Y, Visagie CM. A new family and genus in Dothideales for Aureobasidium-like species isolated from house dust. IMA Fungus 2017; 8:299-315. [PMID: 29242777 PMCID: PMC5729714 DOI: 10.5598/imafungus.2017.08.02.05] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/10/2017] [Indexed: 11/01/2022] Open
Abstract
An international survey of house dust collected from eleven countries using a modified dilution-to-extinction method yielded 7904 isolates. Of these, six strains morphologically resembled the asexual morphs of Aureobasidium and Hormonema (sexual morphs ?Sydowia), but were phylogenetically distinct. A 28S rDNA phylogeny resolved strains as a distinct clade in Dothideales with families Aureobasidiaceae and Dothideaceae their closest relatives. Further analyses based on the ITS rDNA region, β-tubulin, 28S rDNA, and RNA polymerase II second largest subunit confirmed the distinct status of this clade and divided strains among two consistent subclades. As a result, we introduce a new genus and two new species as Zalariaalba and Z. obscura, and a new family to accommodate them in Dothideales. Zalaria is a black yeast-like fungus, grows restrictedly and produces conidiogenous cells with holoblastic synchronous or percurrent conidiation. Zalaria microscopically closely resembles Hormonema by having only one to two loci per conidiogenous cell, but species of our new genus generally has more restricted growth. Comparing the two species, Z. obscura grows faster on lower water activity (aw) media and produces much darker colonies than Z. alba after 7 d. Their sexual states, if extant, are unknown.
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Affiliation(s)
- Zoë Humphries
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6
| | - Keith A Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6.,Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada, K1N 6N5
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, Japan
| | - Cobus M Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6.,Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada, K1N 6N5.,Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
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19
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Tong X, Leung MHY, Wilkins D, Lee PKH. City-scale distribution and dispersal routes of mycobiome in residences. MICROBIOME 2017; 5:131. [PMID: 28978345 PMCID: PMC5628474 DOI: 10.1186/s40168-017-0346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 09/20/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Pathogenic and allergenic bacteria and fungi within the indoors can bring detrimental health effects on the occupants. We previously studied the bacterial communities found in households located throughout Hong Kong as well as the skin surfaces of the occupants. As a complementary study, here, we investigated the fungal communities (mycobiome) in the same residences and occupants and identified factors that are important in shaping their diversity, composition, distribution, and dispersal patterns. RESULTS We observed that common skin and environmental fungal taxa dominated air, surface, and skin samples. Individual and touch frequency strongly and respectively shaped the fungal community structure on occupant skin and residential surfaces. Cross-domain analysis revealed positive correlations between bacterial and fungal community diversity and composition, especially for skin samples. SourceTracker prediction suggested that some fungi can be transferred bidirectionally between surfaces and skin sites, but bacteria showed a stronger dispersal potential. In addition, we detected a modest but significant association between indoor airborne bacterial composition and geographic distance on a city-wide scale, a pattern not observed for fungi. However, the distance-decay effects were more pronounced at shorter local scale for both communities, and airflow might play a prominent role in driving the spatial variation of the indoor airborne mycobiome. CONCLUSIONS Our study suggests that occupants exert a weaker influence on surface fungal communities compared to bacterial communities, and local environmental factors, including air currents, appear to be stronger determinants of indoor airborne mycobiome than ventilation strategy, human occupancy, and room type.
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Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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20
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Abstract
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.
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Affiliation(s)
- J.B. Tanney
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - C.M. Visagie
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood, 0121 Pretoria, South Africa
| | - N. Yilmaz
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - K.A. Seifert
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
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21
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Aspergillus atacamensis and A. salisburgensis: two new halophilic species from hypersaline/arid habitats with a phialosimplex-like morphology. Extremophiles 2017; 21:755-773. [PMID: 28500388 DOI: 10.1007/s00792-017-0941-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/29/2017] [Indexed: 01/11/2023]
Abstract
Halophilic fungal strains isolated from historical wooden staircase in a salt mine in Austria, and from wall biofilm and soil of a cave in the Coastal Range of the hyperarid Atacama Desert in Chile were characterised and described newly as Aspergillus salisburgensis and Aspergillus atacamensis. Morphological characters including solitary phialides producing solitary conidia and conidia in chains and/or heads suggested affinity to Aspergillus subgenus Polypaecilum. Strains required salt for growth, grew optimally on media with 10-25% NaCl and at 15-28 °C. These values are similar to those observed for Aspergillus salinarus comb. nov. (Phialosimplex salinarum), while the ex-type strains of Aspergillus sclerotialis, Aspergillus chlamydosporus and Aspergillus caninus (all belonging to Aspergillus subgen. Polypaecilum) grew optimally at 0-5% NaCl and showed fastest growth at 28-37 °C. Phylogenetic analyses on the basis of rDNA sequences, RAPD-PCR fingerprint patterns, and cellobiohydrolase gene (cbh-I) polymorphism clustered the strains into three groups and supported their taxonomic recognition as A. salinarus, A. atacamensis and A. salisburgensis. On the basis of phylogenetic inferences, also Sagenomella keratitidis is newly combined as Aspergillus keratitidis and inferred as a species of Aspergillus subgenus Polypaecilum.
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Green BJ, Lemons AR, Park Y, Cox-Ganser JM, Park JH. Assessment of fungal diversity in a water-damaged office building. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2017; 14:285-293. [PMID: 27786737 PMCID: PMC6314010 DOI: 10.1080/15459624.2016.1252044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent studies have described fungal communities in indoor environments using gene sequencing-based approaches. In this study, dust-borne fungal communities were elucidated from a water-damaged office building located in the northeastern region of the United States using internal transcribed spacer (ITS) rRNA gene sequencing. Genomic DNA was extracted from 5 mg of floor dust derived from 22 samples collected from either the lower floors (n = 8) or a top floor (n = 14) of the office building. ITS gene sequencing resolved a total of 933 ITS sequences and was clustered into 216 fungal operational taxonomic units (OTUs). Analysis of fungal OTUs at the 97% similarity threshold showed a difference between the lower and top floors that was marginally significant (p = 0.049). Species richness and diversity indices were reduced in the lower floor samples compared to the top floor samples and there was a high degree of compositional dissimilarity within and between the two different areas within the building. Fungal OTUs were placed in the phyla Ascomycota (55%), Basidiomycota (41%), Zygomycota (3%), Glomeromycota (0.4%), Chytridiomycota (0.3%), and unassigned fungi (0.5%). The Ascomycota classes with the highest relative abundances included the Dothideomycetes (30%) and Eurotiomycetes (16%). The Basidiomycota consisted of the classes Ustilaginomycetes (14%), Tremellomycetes (11%), and Agaricomycetes (8%). Sequence reads derived from the plant pathogen Ustilago syntherismae were the most abundant in the analysis as were obligate Basidiomycota yeast species that accounted for 12% and 11% of fungal ITS sequences, respectively. ITS gene sequencing provides additional insight into the diversity of fungal OTUs. These data further highlight the contribution of fungi placed in the phylum Basidiomycota, obligate yeasts, as well as xerophilic species that are typically not resolved using traditional culture methods.
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Affiliation(s)
- Brett J. Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Angela R. Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Yeonmi Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Jean M. Cox-Ganser
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Ju-Hyeong Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
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Lemons AR, Hogan MB, Gault RA, Holland K, Sobek E, Olsen-Wilson KA, Park Y, Park JH, Gu JK, Kashon ML, Green BJ. Microbial rRNA sequencing analysis of evaporative cooler indoor environments located in the Great Basin Desert region of the United States. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:101-110. [PMID: 28091681 PMCID: PMC5450635 DOI: 10.1039/c6em00413j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recent studies conducted in the Great Basin Desert region of the United States have shown that skin test reactivity to fungal and dust mite allergens are increased in children with asthma or allergy living in homes with evaporative coolers (EC). The objective of this study was to determine if the increased humidity previously reported in EC homes leads to varying microbial populations compared to homes with air conditioners (AC). Children with physician-diagnosed allergic rhinitis living in EC or AC environments were recruited into the study. Air samples were collected from the child's bedroom for genomic DNA extraction and metagenomic analysis of bacteria and fungi using the Illumina MiSeq sequencing platform. The analysis of bacterial populations revealed no major differences between EC and AC sampling environments. The fungal populations observed in EC homes differed from AC homes. The most prevalent species discovered in AC environments belonged to the genera Cryptococcus (20%) and Aspergillus (20%). In contrast, the most common fungi identified in EC homes belonged to the order Pleosporales and included Alternaria alternata (32%) and Phoma spp. (22%). The variations in fungal populations provide preliminary evidence of the microbial burden children may be exposed to within EC environments in this region.
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Affiliation(s)
- Angela R Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, WV 26505, USA.
| | - Mary Beth Hogan
- Department of Pediatrics, Pediatrics Center, University of Nevada School of Medicine, Las Vegas, NV, USA
| | - Ruth A Gault
- Department of Microbiology and Immunology, Center for Molecular Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Kathleen Holland
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Kimberly A Olsen-Wilson
- Department of Pediatrics, Center for Molecular Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Yeonmi Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ju-Hyeong Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ja Kook Gu
- Biostatistics and Epidemiology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Michael L Kashon
- Biostatistics and Epidemiology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Brett J Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, WV 26505, USA.
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Broadwater K, de Perio MA, Roberts J, Burton NC, Lemons AR, Green BJ, Brueck SE. Investigating a persistent odor at an aircraft seat manufacturer. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2016; 13:D159-65. [PMID: 27494786 PMCID: PMC5511731 DOI: 10.1080/15459624.2016.1183017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An aircraft seat manufacturing company requested a NIOSH health hazard evaluation to help identify a strong odor that had persisted throughout the facility for over a year. Employees reported experiencing health effects thought to be related to the odor. We collected and analyzed area air samples for volatile organic compounds, endotoxin, bacterial and fungal metagenome, and metalworking fluid aerosol. Bulk metalworking fluid samples were analyzed for endotoxin, bacterial and fungal metagenome, and viable bacteria and fungus. We also evaluated the building ventilation systems and water diversion systems. Employees underwent confidential medical interviews about work practices, medical history, and health concerns. Based on our analyses, the odor was likely 2-methoxy-3,5-dimethylpyrazine. This pyrazine was found in air samples across the facility and originated from bacteria in the metalworking fluid. We did not identify bacteria known to produce the compound but bacteria from the same Proteobacteria order were found as well as bacteria from orders known to produce other pyrazines. Chemical and biological contaminants and odors could have contributed to health symptoms reported by employees, but it is likely that the symptoms were caused by several factors. We provided several recommendations to eliminate the odor including washing and disinfecting the metalworking machines and metalworking fluid recycling equipment, discarding all used metalworking fluid, instituting a metalworking fluid maintenance program at the site, and physically isolating the metalworking department from other departments.
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Affiliation(s)
- Kendra Broadwater
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Division of Surveillance, Hazard Evaluations and Field Studies, Hazard Evaluations and Technical Assistance Branch, Cincinnati, Ohio
| | - Marie A. de Perio
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Division of Surveillance, Hazard Evaluations and Field Studies, Hazard Evaluations and Technical Assistance Branch, Cincinnati, Ohio
| | - Jennifer Roberts
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Division of Applied Research and Technology, Chemical Exposure and Monitoring Branch, Cincinnati, Ohio
| | - Nancy C. Burton
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Division of Surveillance, Hazard Evaluations and Field Studies, Hazard Evaluations and Technical Assistance Branch, Cincinnati, Ohio
| | - Angela R. Lemons
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Health Effects Laboratory Division, Allergy and Clinical Immunology Branch, Morgantown, West Virginia
| | - Brett J. Green
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Health Effects Laboratory Division, Allergy and Clinical Immunology Branch, Morgantown, West Virginia
| | - Scott E. Brueck
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Division of Surveillance, Hazard Evaluations and Field Studies, Hazard Evaluations and Technical Assistance Branch, Cincinnati, Ohio
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Yan D, Zhang T, Su J, Zhao LL, Wang H, Fang XM, Zhang YQ, Liu HY, Yu LY. Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days. Front Microbiol 2016; 7:487. [PMID: 27148180 PMCID: PMC4830834 DOI: 10.3389/fmicb.2016.00487] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/23/2016] [Indexed: 11/13/2022] Open
Abstract
To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.
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Affiliation(s)
- Dong Yan
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Jing Su
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Li-Li Zhao
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Hao Wang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Xiao-Mei Fang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Yu-Qin Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Hong-Yu Liu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Li-Yan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
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Piñar G, Tafer H, Sterflinger K, Pinzari F. Amid the possible causes of a very famous foxing: molecular and microscopic insight into Leonardo da Vinci's self-portrait. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:849-59. [PMID: 26111623 PMCID: PMC4959533 DOI: 10.1111/1758-2229.12313] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
Leonardo da Vinci's self-portrait is affected by foxing spots. The portrait has no fungal or bacterial infections in place, but is contaminated with airborne spores and fungal material that could play a role in its disfigurement. The knowledge of the nature of the stains is of great concern because future conservation treatments should be derived from scientific investigations. The lack of reliable scientific data, due to the non-culturability of the microorganisms inhabiting the portrait, prompted the investigation of the drawing using non-invasive and micro-invasive sampling, in combination with scanning electron microscope (SEM) imaging and molecular techniques. The fungus Eurotium halophilicum was found in foxing spots using SEM analyses. Oxalates of fungal origin were also documented. Both findings are consistent with the hypothesis that tonophilic fungi germinate on paper metabolizing organic acids, oligosaccharides and proteic compounds, which react chemically with the material at a low water activity, forming brown products and oxidative reactions resulting in foxing spots. Additionally, molecular techniques enabled a screening of the fungi inhabiting the portrait and showed differences when different sampling techniques were employed. Swabs samples showed a high abundance of lichenized Ascomycota, while the membrane filters showed a dominance of Acremonium sp. colonizing the drawing.
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Affiliation(s)
- Guadalupe Piñar
- Department of Biotechnology, Vienna Institute of Biotechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 11, Vienna, 1190, Austria
| | - Hakim Tafer
- Department of Biotechnology, Vienna Institute of Biotechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 11, Vienna, 1190, Austria
| | - Katja Sterflinger
- Department of Biotechnology, Vienna Institute of Biotechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 11, Vienna, 1190, Austria
| | - Flavia Pinzari
- Istituto Centrale per il Restauro e la Conservazione del Patrimonio Archivistico e Librario (ICRCPAL), Ministero per i Beni e le Attivita Culturali, Via Milano 76, Rome, 00184, Italy.
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27
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Ciaccio CE, Barnes C, Kennedy K, Chan M, Portnoy J, Rosenwasser L. Home dust microbiota is disordered in homes of low-income asthmatic children. J Asthma 2015; 52:873-80. [PMID: 26512904 DOI: 10.3109/02770903.2015.1028076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Exposure to microorganisms has repeatedly been found to influence development of atopic diseases, such as asthma. Innovative techniques have been developed that can comprehensively characterize microbial communities. The objective of this study was to characterize the home microbiota of asthmatic children utilizing 16S rRNA-based phylogenetic analysis by microarray. METHODS In this cross-sectional study, DNA was extracted from home dust and bacterial 16S rRNA genes amplified. Bacterial products were hybridized to the PhyloChip Array and scanned using a GeneArray scanner (Affymetrix, Santa Clara, CA). The Adonis test was used to determine significant differences in the whole microbiome. Welch's t-test was used to determine significant abundance differences and genus-level richness differences. RESULTS Nineteen homes were included in the analysis (14 asthma and five no asthma). About 1741 operational taxonomic units (OTUs) were found in at least one sample. Bacterial genus richness did not differ in the homes of asthmatics and non-asthmatics (p = 0.09). The microbial profile was significantly different between the two groups (p = 0.025). All the top 12 OTUs with significant abundance differences were increased in homes of asthmatics and belonged to one of the five phyla (p = 0.001 to p = 7.2 × 10(-6)). Nearly half of significant abundance differences belonged to the phylum Cyanobacteria or Proteobacteria. CONCLUSIONS These results suggest that home dust has a characteristic microbiota which is disturbed in the homes of asthmatics, resulting in a particular abundance of Cyanobacteria and Proteobacteria. Further investigations are needed which utilize high-throughput technology to further clarify how home microbial exposures influence human health and disease.
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Affiliation(s)
- Christina E Ciaccio
- a Department of Pediatrics and the Center for Environmental Health , Children's Mercy Hospital , Kansas City , MO , USA
| | - Charles Barnes
- a Department of Pediatrics and the Center for Environmental Health , Children's Mercy Hospital , Kansas City , MO , USA
| | - Kevin Kennedy
- a Department of Pediatrics and the Center for Environmental Health , Children's Mercy Hospital , Kansas City , MO , USA
| | - Marcia Chan
- a Department of Pediatrics and the Center for Environmental Health , Children's Mercy Hospital , Kansas City , MO , USA
| | - Jay Portnoy
- a Department of Pediatrics and the Center for Environmental Health , Children's Mercy Hospital , Kansas City , MO , USA
| | - Lanny Rosenwasser
- a Department of Pediatrics and the Center for Environmental Health , Children's Mercy Hospital , Kansas City , MO , USA
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Jančič S, Nguyen HDT, Frisvad JC, Zalar P, Schroers HJ, Seifert KA, Gunde-Cimerman N. A Taxonomic Revision of the Wallemia sebi Species Complex. PLoS One 2015; 10:e0125933. [PMID: 26017053 PMCID: PMC4446336 DOI: 10.1371/journal.pone.0125933] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/25/2015] [Indexed: 12/15/2022] Open
Abstract
Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS) regions, DNA replication licensing factor (MCM7), pre-rRNA processing protein (TSR1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and a new marker 3´-phosphoadenosine-5´-phosphatase (HAL2), confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W. tropicalis. The species differ in their conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. A key to all currently accepted Wallemia species is provided that allow their identification on the basis of physiological, micromorphological and culture characters.
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Affiliation(s)
- Sašo Jančič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Hai D. T. Nguyen
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jens C. Frisvad
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Keith A. Seifert
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
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Gabriel MF, Postigo I, Gutiérrez-Rodríguez A, Suñén E, Tomaz CT, Martínez J. Development of a PCR-based tool for detecting immunologically relevant Alt a 1 and Alt a 1 homologue coding sequences. Med Mycol 2015; 53:636-42. [PMID: 25877667 DOI: 10.1093/mmy/myv022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 11/12/2022] Open
Abstract
Alt a 1 has been recognized as the most important allergen produced by the Pleosporaceae family and is a risk factor for asthma development and/or exacerbation. The aim of this study was to develop a detection tool that is highly specific for species that produced airborne Alt a 1. Based on the highly conserved internal nucleotide region of the several Alt a 1 sequences that are available in GenBank, a pair of primers (Alta1CF/Alta1CR) was designed. A set of primers used by other authors for the production of recombinant Alt a 1 (A21F/A21R) was also tested. The molecular analyses were based on the polymerase chain reaction (PCR) amplification and sequencing of the cDNA that was obtained from thirteen common fungal species. The PCR system that utilized Alta1CF/Alta1CR was highly specific, sensitive, and was able to detect an amplicon of approximately 180 bp from Alt a 1 and Alt a 1-like encoding genes from A. alternata, A. tenuissima, A. infectoria, U. botrytis, and S. botryosum. In contrast, the A21F/A21R primers were specific for the very close taxonomically related species A. alternata and A. tenuissima. Thus, this rapid, sensitive, and specific detection tool can be used to assess Alt a 1 exposure levels and to inform the implementation of the appropriate public health measures.
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Affiliation(s)
- M F Gabriel
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria, Spain Department of Chemistry and CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - I Postigo
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria, Spain
| | - A Gutiérrez-Rodríguez
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria, Spain
| | - E Suñén
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria, Spain
| | - C T Tomaz
- Department of Chemistry and CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - J Martínez
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria, Spain
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Ferro M, Antonio EA, Souza W, Bacci M. ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences. BMC Res Notes 2014; 7:857. [PMID: 25430816 PMCID: PMC4258023 DOI: 10.1186/1756-0500-7-857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 11/19/2014] [Indexed: 11/17/2022] Open
Abstract
Background Studies on fungal diversity and ecology aim to identify fungi and to investigate their interactions with each other and with the environment. DNA sequence-based tools are essential for these studies because they can speed up the identification process and access greater fungal diversity than traditional methods. The nucleotide sequence encoding for the internal transcribed spacer (ITS) of the nuclear ribosomal RNA has recently been proposed as a standard marker for molecular identification of fungi and evaluation of fungal diversity. However, the analysis of large sets of ITS sequences involves many programs and steps, which makes this task intensive and laborious. Findings We developed the web-based pipeline ITScan, which automates the analysis of fungal ITS sequences generated either by Sanger or Next Generation Sequencing (NGS) platforms. Validation was performed using datasets containing ca. 2,000 to 40,000 sequences each. Conclusions ITScan is an online and user-friendly automated pipeline for fungal diversity analysis and identification based on ITS sequences. It speeds up a process which would otherwise be repetitive and time-consuming for users. The ITScan tool and documentation are available at http://evol.rc.unesp.br:8083/itscan.
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Affiliation(s)
- Milene Ferro
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, UNESP - Univ Estadual Paulista, Rio Claro SP 13506-900, Brazil.
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Damm U, O'Connell R, Groenewald J, Crous P. The Colletotrichum destructivum species complex - hemibiotrophic pathogens of forage and field crops. Stud Mycol 2014; 79:49-84. [PMID: 25492986 PMCID: PMC4255528 DOI: 10.1016/j.simyco.2014.09.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Colletotrichum destructivum is an important plant pathogen, mainly of forage and grain legumes including clover, alfalfa, cowpea and lentil, but has also been reported as an anthracnose pathogen of many other plants worldwide. Several Colletotrichum isolates, previously reported as closely related to C. destructivum, are known to establish hemibiotrophic infections in different hosts. The inconsistent application of names to those isolates based on outdated species concepts has caused much taxonomic confusion, particularly in the plant pathology literature. A multilocus DNA sequence analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 83 isolates of C. destructivum and related species revealed 16 clades that are recognised as separate species in the C. destructivum complex, which includes C. destructivum, C. fuscum, C. higginsianum, C. lini and C. tabacum. Each of these species is lecto-, epi- or neotypified in this study. Additionally, eight species, namely C. americae-borealis, C. antirrhinicola, C. bryoniicola, C. lentis, C. ocimi, C. pisicola, C. utrechtense and C. vignae are newly described.
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Affiliation(s)
- U. Damm
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - R.J. O'Connell
- UMR1290 BIOGER-CPP, INRA-AgroParisTech, 78850 Thiverval-Grignon, France
| | - J.Z. Groenewald
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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