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)

Abstract

A peer-reviewed open-access journal MycoKeysLaunched to accelerate biodiversity research RESEARCH ARTICLEKessy Abarenkov et al. / MycoKeys 16: 1-15 (2016) Abstract Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data -for example, "retrieve all fungal sequences recovered from bathrooms" -a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

“…Important work has already been done at the UNITE database to facilitate third party metadata annotations for ITS sequence data using the PlutoF workbench ( 37 ). This resulted in annotation efforts focused on specific standards, such the MIxS-Built Environmental standard ( 38 ) and a call for additional taxonomic information on the most commonly found unidentified ITS sequence clusters from the environment ( 39 ). To compliment these efforts in the NCBI public databases we decided to append basic information such as host, isolation source and location for Trichoderma RefSeq records.…”

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

“…; Abarenkov et al . ). Thus, additional research efforts targeting reference database gaps and improved database curation techniques are also warranted.…”

AspergillussubgenusPolypaecilumfrom the built environment

“…A better understanding of fungal ecology, biodiversity and species concepts, and improved barcoding abilities (e.g. : Abarenkov et al. 2016 ), will ameliorate the current resolution of ENAS studies, facilitate source tracking of organisms in the built environment, and progress our knowledge of interactions between occupants and fungi.…”