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

R. Henrik Nilsson*, Andy F.S. Taylor, Rachel I. Adams, Christiane Baschien, Johan Bengtsson-Palme, Patrik Cangren, Claudia Coleine, Heide Marie Daniel, Sydney I. Glassman, Yuuri Hirooka, Laszlo Irinyi, Reda Iršenaite, Pedro M. Martin-Sanchez, Wieland Meyer, Seung Yoon Oh, Jose Paulo Sampaio, Keith A. Seifert, Frantisek Sklenář, Dirk Stubbe, Sung Oui SuhRichard Summerbell, Sten Svantesson, Martin Unterseher, Cobus M. Visagie, Michael Weiss, Joyce H.C. Woudenberg, Christian Wurzbacher, Silke Van Den Wyngaert, Neriman Yilmaz, Andrey Yurkov, Urmas Kõljalg, Kessy Abarenkov

*Corresponding author for this work

Research output: Contribution to journalArticle

7 Citations (Scopus)
6 Downloads (Pure)

Abstract

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.

Original languageEnglish
Pages (from-to)65-82
Number of pages18
JournalMycoKeys
Volume28
DOIs
Publication statusPublished - 8 Jan 2018

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metadata
fungus
fungi
Talaromyces
Acremonium
allergy
Cladosporium
barcoding
Alternaria
Penicillium
hypersensitivity
DNA
substrate
public
built environment
resource

Keywords

  • Built environment
  • Fungi
  • Indoor mycobiome
  • Metadata
  • Molecular identification
  • Open data
  • Sequence annotation
  • Systematics
  • Taxonomy

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Plant Science

Cite this

Taxonomic annotation of public fungal ITS sequences from the built environment - A report from an April 10-11, 2017 workshop (Aberdeen, UK). / Nilsson, R. Henrik; Taylor, Andy F.S.; Adams, Rachel I.; Baschien, Christiane; Bengtsson-Palme, Johan; Cangren, Patrik; Coleine, Claudia; Daniel, Heide Marie; Glassman, Sydney I.; Hirooka, Yuuri; Irinyi, Laszlo; Iršenaite, Reda; Martin-Sanchez, Pedro M.; Meyer, Wieland; Oh, Seung Yoon; Sampaio, Jose Paulo; Seifert, Keith A.; Sklenář, Frantisek; Stubbe, Dirk; Suh, Sung Oui; Summerbell, Richard; Svantesson, Sten; Unterseher, Martin; Visagie, Cobus M.; Weiss, Michael; Woudenberg, Joyce H.C.; Wurzbacher, Christian; Van Den Wyngaert, Silke; Yilmaz, Neriman; Yurkov, Andrey; Kõljalg, Urmas; Abarenkov, Kessy.

In: MycoKeys, Vol. 28, 08.01.2018, p. 65-82.

Research output: Contribution to journalArticle

Nilsson, RH, Taylor, AFS, Adams, RI, Baschien, C, Bengtsson-Palme, J, Cangren, P, Coleine, C, Daniel, HM, Glassman, SI, Hirooka, Y, Irinyi, L, Iršenaite, R, Martin-Sanchez, PM, Meyer, W, Oh, SY, Sampaio, JP, Seifert, KA, Sklenář, F, Stubbe, D, Suh, SO, Summerbell, R, Svantesson, S, Unterseher, M, Visagie, CM, Weiss, M, Woudenberg, JHC, Wurzbacher, C, Van Den Wyngaert, S, Yilmaz, N, Yurkov, A, Kõljalg, U & Abarenkov, K 2018, 'Taxonomic annotation of public fungal ITS sequences from the built environment - A report from an April 10-11, 2017 workshop (Aberdeen, UK)', MycoKeys, vol. 28, pp. 65-82. https://doi.org/10.3897/mycokeys.28.20887
Nilsson, R. Henrik ; Taylor, Andy F.S. ; Adams, Rachel I. ; Baschien, Christiane ; Bengtsson-Palme, Johan ; Cangren, Patrik ; Coleine, Claudia ; Daniel, Heide Marie ; Glassman, Sydney I. ; Hirooka, Yuuri ; Irinyi, Laszlo ; Iršenaite, Reda ; Martin-Sanchez, Pedro M. ; Meyer, Wieland ; Oh, Seung Yoon ; Sampaio, Jose Paulo ; Seifert, Keith A. ; Sklenář, Frantisek ; Stubbe, Dirk ; Suh, Sung Oui ; Summerbell, Richard ; Svantesson, Sten ; Unterseher, Martin ; Visagie, Cobus M. ; Weiss, Michael ; Woudenberg, Joyce H.C. ; Wurzbacher, Christian ; Van Den Wyngaert, Silke ; Yilmaz, Neriman ; Yurkov, Andrey ; Kõljalg, Urmas ; Abarenkov, Kessy. / Taxonomic annotation of public fungal ITS sequences from the built environment - A report from an April 10-11, 2017 workshop (Aberdeen, UK). In: MycoKeys. 2018 ; Vol. 28. pp. 65-82.
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abstract = "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.",
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AU - Daniel, Heide Marie

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