Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK)

. 2018 ; (28) : 65-82. [epub] 20180108

Status PubMed-not-MEDLINE Jazyk angličtina Země Bulharsko Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid29559822

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.

ATCC 10801 University Blvd Manassas Virginia 20110 USA

BCCM IHEM Scientific Institute of Public Health WIV ISP Juliette Wytsmanstraat 14 1050 Brussels Belgium

Biodiversity Ottawa Research and Development Centre Agriculture and Agri Food Canada Ottawa ON Canada K1A 0C6

Biosystematics Division ARC Plant Health and Protection P BagX134 Queenswood 0121 Pretoria South Africa

Bundesanstalt für Materialforschung und prüfung Department 4 Materials and Environment Unter den Eichen 87 12205 Berlin Germany

Dalla Lana School of Public Health University of Toronto Health Sciences Building 155 College Street 6th floor Toronto Ontario Canada M5T 3M7

Department of Biological and Environmental Sciences University of Gothenburg Box 463 405 30 Göteborg Sweden

Department of Biology University of Ottawa 30 Marie Curie Ottawa ON Canada K1N 6N5

Department of Botany Faculty of Science Charles University Prague Czech Republic

Department of Clinical Plant Science Faculty of Bioscience Hosei University 3 7 2 Kajino cho Koganei Tokyo Japan 184 8584

Department of Ecological and Biological Sciences University of Tuscia Viterbo 01100 Italy

Department of Ecology and Evolutionary Biology UC Irvine Irvine CA 92697 USA

Department of Experimental Limnology Leibniz Institute of Freshwater Ecology and Inland Fisheries Alte Fischerhuette 2 D 16775 Stechlin Germany

Department of Infectious Diseases Institute of Biomedicine The Sahlgrenska Academy University of Gothenburg Guldhedsgatan 10 SE 413 46 Gothenburg Sweden

Department of Plant Pathology and Microbiology and Institute of Integrative Genome Biology University of California Riverside Riverside 92501 CA USA

Evangelisches Schulzentrum Martinschule Max Planck Str 7 17491 Greifswald Germany

Gothenburg Global Biodiversity Centre Box 461 SE 405 30 Göteborg Sweden

Institute of Botany Nature Research Centre Žaliųjų ežerų Str 49 08406 Vilnius Lithuania

Institute of Microbiology Academy of Sciences of the Czech Republic v v i Prague Czech Republic

Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures Inhoffenstrasse 7 B 38124 Braunschweig Germany

Plant and Microbial Biology University of California 94720 Berkeley California USA

School of Biological Sciences Seoul National University Seoul Republic of Korea

Sporometrics 219 Dufferin Street Suite 20C Toronto Ontario Canada M6K 1Y9

Steinbeis Innovationszentrum Organismische Mykologie und Mikrobiologie Vor dem Kreuzberg 17 72070 Tübingen Germany

Sydney Medical School Westmead Hospital Molecular Mycology Research Laboratory Centre for Infectious Diseases and Microbiology Sydney Australia

The James Hutton Institute and University of Aberdeen Aberdeen United Kingdom

UCIBIO REQUIMTE DCV Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa 2829 516 Caparica Portugal

Université catholique de Louvain Earth and Life Institute Applied Microbiology BCCM MUCL Louvain la Neuve Belgium

University of Sydney Marie Bashir Institute for Infectious Diseases and Biosecurity Sydney Australia

University of Tartu Tartu Estonia

Westerdijk Fungal Biodiversity Institute Uppsalalaan 8 3584 CT Utrecht The Netherlands

Westmead Institute for Medical Research Westmead Australia

Zobrazit více v PubMed

Abarenkov K, Tedersoo L, Nilsson RH et al. (2010) PlutoF - a web-based workbench for ecological and taxonomical research, with an online implementation for fungal ITS sequences. Evolutionary Bioinformatics 6: 189–196. 10.4137/EBO.S6271 DOI

Abarenkov K, Adams RI, Laszlo I et al. (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard - a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1–16. 10.3897/mycokeys.16.10000 DOI

Adams RI, Miletto M, Taylor JW, Bruns TD. (2013) Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. The ISME Journal 7(7): 1262–1273. 10.1038/ismej.2013.28 PubMed DOI PMC

Adams RI, Bhangar S, Dannemiller KC et al. (2016) Ten questions concerning the microbiomes of buildings. Building and Environment 109: 224–234. 10.1016/j.buildenv.2016.09.001 DOI

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research 25(17): 3389–3402. 10.1093/nar/25.17.3389 PubMed DOI PMC

Amend AS, Seifert KA, Samson R, Bruns TD. (2010) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proceedings of the National Academy of Sciences 107(31): 13748–13753. 10.1073/pnas.1000454107 PubMed DOI PMC

Benedict K, Chiller TM, Mody RK. (2016) Invasive fungal infections acquired from contaminated food or nutritional supplements: a review of the literature. Foodborne Pathogens and Disease 13(7): 343–349. 10.1089/fpd.2015.2108 PubMed DOI PMC

Blackwell M. (2011) The Fungi: 1, 2, 3… 5.1 million species? American Journal of Botany 98(3): 426–438. 10.3732/ajb.1000298 PubMed DOI

Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E. (2005) Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society of London B: Biological Sciences 360(1462): 1935–1943. 10.1098/rstb.2005.1725 PubMed DOI PMC

Cardinale M, Kaiser D, Lueders T, Schnell S, Egert M. (2017) Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species. Scientific Reports 7: 5791. 10.1038/s41598-017-06055-9 PubMed DOI PMC

Cochrane G, Karsch-Mizrachi I, Takagi T, International Nucleotide Sequence Database Collaboration. (2016) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Research 44(D1): D48–D50. 10.1093/nar/gkv1323 PubMed DOI PMC

Daniel HM, Lachance MA, Kurtzman CP. (2014) On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription. Antonie van Leeuwenhoek 106(1): 67–84. 10.1007/s10482-014-0170-z PubMed DOI

Flannigan B, Samson RA, Miller JD. (2011) Microorganisms in home and indoor work environments: diversity, health impacts, investigation and control. CRC Press. 10.1201/b10838 DOI

Garnier L, Valence F, Pawtowski A et al. (2017) Diversity of spoilage fungi associated with various French dairy products. International Journal of Food Microbiology 241: 191–197. 10.1016/j.ijfoodmicro.2016.10.026 PubMed DOI

Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA. (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18(12): 1641–1649. 10.1093/bioinformatics/18.12.1641 PubMed DOI

Glass EM, Dribinsky Y, Yilmaz P et al. (2014) MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME Journal 8(1): 1–3. 10.1038/ismej.2013.176 PubMed DOI PMC

Houbraken J, Frisvad JC, Seifert KA, Overy DP, Tuthill DM, Valdez JG, Samson RA. (2012) New penicillin-producing Penicillium species and an overview of section Chrysogena. Persoonia 29: 78–100. 10.3767/003158512X660571 PubMed DOI PMC

Hyde KD, Udayanga D, Manamgoda DS et al. (2013) Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Current Research in Environmental and Applied Mycology 3(1): 1–32. 10.5943/cream/3/1/1 DOI

Irinyi L, Serena C, Garcia-Hermoso D et al. (2015) International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database -the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Medical Mycology 53(4): 313–337. 10.1093/mmy/myv008 PubMed DOI

Jančič S, Nguyen HD, Frisvad JC, Zalar P, Schroers HJ, Seifert KA, Gunde-Cimerman N. (2015) A taxonomic revision of the Wallemiasebi species complex. PLOS ONE 10(5): e0125933. 10.1371/journal.pone.0125933 PubMed DOI PMC

Jurjević Ž, Peterson SW, Horn BW. (2012) AspergillussectionVersicolores: nine new species and multilocus DNA sequence based phylogeny. IMA Fungus 3(1): 59–795. 10.5598/imafungus.2012.03.01.07 PubMed DOI PMC

Kang S, Mansfield MAM, Park B et al. (2010) The promise and pitfalls of sequence-based identification of plant pathogenic fungi and oomycetes. Phytopathology 100(8): 732–737. 10.1094/PHYTO-100-8-0732 PubMed DOI

Khan AH, Karuppayil SM. (2012) Fungal pollution of indoor environments and its management. Saudi Journal of Biological Sciences 19(4): 405–426. 10.1016/j.sjbs.2012.06.002 PubMed DOI PMC

Kurtzman CP. (2014) Use of gene sequence analyses and genome comparisons for yeast systematics. International Journal of Systematic and Evolutionary Microbiology 64(2): 325–332. 10.1099/ijs.0.054197-0 PubMed DOI

Kõljalg U, Nilsson RH, Abarenkov K et al. (2013) Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology 22(21): 5271–5277. 10.1111/mec.12481 PubMed DOI

Liu XZ, Wang QM, Göker M et al. (2015) Towards an integrated phylogenetic classification of the Tremellomycetes. Studies in Mycology 81: 85–147. 10.1016/j.simyco.2015.12.001 PubMed DOI PMC

Mensah-Attipoe J, Reponen T, Veijalainen AM et al. (2016) Comparison of methods for assessing temporal variation of growth of fungi on building materials. Microbiology 162(11): 1895–1903. 10.1099/mic.0.000372 PubMed DOI

Meyer L, Brischke C, Treu A, Larsson-Brelid P. (2016) Critical moisture conditions for fungal decay of modified wood by basidiomycetes as detected by pile tests. Holzforschung 70(4): 331–339. 10.1515/hf-2015-0046, DOI

Nevalainen A, Täubel M, Hyvärinen A. (2015) Indoor fungi: companions and contaminants. Indoor Air 25(2): 125–156. 10.1111/ina.12182 PubMed DOI

Nguyen HD, Jančič S, Meijer M, Tanney JB, Zalar P, Gunde-Cimerman N, Seifert KA. (2015) Application of the phylogenetic species concept to Wallemiasebi from house dust and indoor air revealed by multi-locus genealogical concordance. PLOS ONE 10(3): e0120894. 10.1371/journal.pone.0120894 PubMed DOI PMC

Nilsson RH, Tedersoo L, Abarenkov K et al. (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37–63. 10.3897/mycokeys.4.3606 DOI

Nilsson RH, Tedersoo L, Ryberg M et al. (2015) A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments 30(2): 145–150. 10.1264/jsme2.ME14121 PubMed DOI PMC

Nilsson RH, Wurzbacher C, Bahram M et al. (2016) Top 50 most wanted fungi. MycoKeys 12: 29–40. 10.3897/mycokeys.12.7553 PubMed DOI PMC

Nilsson RH, Sánchez-García M, Ryberg MK, Abarenkov K, Wurzbacher C, Kristiansson E. (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13–24. 10.3897/mycokeys.26.14591 DOI

Norbäck D, Hashim JH, Cai G-H, Hashim Z, Ali F, Bloom E, Larsson L. (2016) Rhinitis, ocular, throat and dermal symptoms, headache and tiredness among students in schools from Johor Bahru, Malaysia: associations with fungal DNA and mycotoxins in classroom dust. PLoS ONE 11(2): e0147996. 10.1371/journal.pone.0147996 PubMed DOI PMC

O’Donnell K, Ward TJ, Robert VARG, Crous PW, Geiser DM, Kang S. (2015) DNA sequence-based identification of Fusarium: current status and future directions. Phytoparasitica 43(5): 583–595. 10.1007/s12600-015-0484-z DOI

O’Leary NA, Wright MW, Brister JR et al. (2015) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1): D733–D745. 10.1093/nar/gkv1189 PubMed DOI PMC

Schoch CL, Seifert KA, Huhndorf S et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences USA 109(16): 6241–6246. 10.1073/pnas.1117018109 PubMed DOI PMC

Stamper CE, Hoisington AJ, Gomez OM et al. (2016) The microbiome of the built environment and human behavior: implications for emotional health and well-being in postmodern western societies. International Review of Neurobiology 131: 289–323. 10.1016/bs.irn.2016.07.006 PubMed DOI

Taylor DL, Hollingsworth TN, McFarland JW, Lennon NJ, Nusbaum C, Ruess RW. (2014) A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecological Monographs 84(1): 3–20. 10.1890/12-1693.1 DOI

Tedersoo L, Abarenkov K, Nilsson RH et al. (2011) Tidying up International Nucleotide Sequence Databases: ecological, geographical, and sequence quality annotation of ITS sequences of mycorrhizal fungi. PLoS ONE 6(9): e24940. 10.1371/journal.pone.0024940 PubMed DOI PMC

Tischer C, Weikl F, Probst AJ, Standl M, Heinrich J, Pritsch K. (2016) Urban dust microbiome: impact on later atopy and wheezing. Environmental Health Perspectives 124(12): 1919–1923. 10.1289/EHP158 PubMed DOI PMC

Visagie CM, Houbraken J, Frisvad JC, Hong SB, Klaassen CHW, Perrone G, Seifert KA, Varga J, Samson RA. (2014) Identification and nomenclature of the genus Penicillium. Studies in Mycology 78: 343–371. 10.1016/j.simyco.2014.09.001 PubMed DOI PMC

Visagie CM, Yilmaz N, Renaud JB, Sumarah MW, Hubka V, Frisvad JC, Chen AJ, Meijer M, Seifert KA. (2017) A survey of xerophilic Aspergillus from indoor environment, including descriptions of two new section Aspergillus species producing eurotium-like sexual states. MycoKeys 19: 1–30. 10.3897/mycokeys.19.11161 DOI

Wang QM, Yurkov AM, Göker M et al. (2015) Phylogenetic classification of yeasts and related taxa within Pucciniomycotina. Studies in Mycology 81: 149–189. 10.1016/j.simyco.2015.12.002 PubMed DOI PMC

WHO (2009) WHO guidelines for indoor air quality: dampness and mould. WHO Europe, Copenhagen, 228 pp. PubMed

Yilmaz N, Visagie CM, Houbraken J, Frisvad JC, Samson RA. (2014) Polyphasic taxonomy of the genus Talaromyces. Studies in Mycology 78(1): 175–341. 10.1016/j.simyco.2014.08.001 PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

    Možnosti archivace