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

By

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
Laszlo, Irinyi
Iršėnaitė, Reda
Martin-Sanchez, Pedro M.
Meyer, Wieland
Oh, Seung-Yoon
Sampaio,‏ ‎José Paulo Nunes de Sousa, 1963-
Seifert, Keith
Sklenář, Frantisek
Dirk Stubbe, Dirk Stubbe
Suh, Sung-Oui
Summerbell, Richard
Svantesson, Sten
Unterseher, Martin
Visagie, Cobus
Weiss, Michael
Woudenberg, Joyce
Wurzbacher, Christian
Wyngaert, Silke van den
Yilmaz, Neriman
Yurkov, Andrey
Kõljalg, Urmas, 1961-
Abarenkov, Kessy

Type

Article

Date of Publication

2018

Original Publication

Subterranean Biology

Volume

28

Pages

65-82

Subjects

built environment , Fungi , Indoor mycobiome , metadata , molecular identification , open data , sequence annotation , systematics , taxonomy

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers

Identifiers

DOI: https://doi.org/10.3897/mycokeys.28.20887

 

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.