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.
Highlights
The built environment presents dry, harsh conditions for fungal life, and traditional estimates of “indoor” fungi run in the low hundreds (Flannigan et al 2011; Khan and Karuppayil 2012)
General taxonomic progress and studies based on high-throughput sequencing (HTS) of amplicons are changing our view of the built environment as a biologically depauperate habitat
Many of the common indoor species have been divided into numerous new species, thereby increasing the number of indoor species considerably (e.g., Aspergillus versicolor divided into ten new species (Jurjević et al 2012), Penicillium chrysogenum into five species (Houbraken et al 2012), and Wallemia sebi into four species (Nguyen et al 2015, Jančič et al 2015))
Summary
The built environment presents dry, harsh conditions for fungal life, and traditional estimates of “indoor” fungi run in the low hundreds (Flannigan et al 2011; Khan and Karuppayil 2012). In a global study of indoor dust, Amend et al (2010) found no less than 4,473 approximately species-level fungal operational taxonomic units (OTUs; Blaxter et al 2005) distributed across more than 20 different fungal orders. Understanding the built mycobiome, becomes a matter of understanding a much larger number of species than those traditionally considered to form the core indoor fungi. Many of the common indoor species have been divided into numerous new species, thereby increasing the number of indoor species considerably (e.g., Aspergillus versicolor divided into ten new species (Jurjević et al 2012), Penicillium chrysogenum into five species (Houbraken et al 2012), and Wallemia sebi into four species (Nguyen et al 2015, Jančič et al 2015))
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