Mycobiome diversity: high-throughput sequencing and identification of fungi

RH Nilsson, S Anslan, M Bahram… - Nature Reviews …, 2019 - nature.com
Fungi are major ecological players in both terrestrial and aquatic environments by cycling
organic matter and channelling nutrients across trophic levels. High-throughput sequencing …

The mycobiome in health and disease: emerging concepts, methodologies and challenges

PY Tiew, M Mac Aogain, NABM Ali, KX Thng, K Goh… - Mycopathologia, 2020 - Springer
Fungal disease is an increasingly recognised global clinical challenge associated with high
mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity …

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

RH Nilsson, KH Larsson, AFS Taylor… - Nucleic acids …, 2019 - academic.oup.com
Abstract UNITE (https://unite. ut. ee/) is a web-based database and sequence management
environment for the molecular identification of fungi. It targets the formal fungal barcode—the …

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

RT Richardson, J Bengtsson‐Palme… - Molecular Ecology …, 2017 - Wiley Online Library
The taxonomic classification of DNA sequences has become a critical component of
numerous ecological research applications; however, few studies have evaluated the …

 The curse of the uncultured fungus

K Abarenkov, E Kristiansson, M Ryberg… - …, 2022 - pmc.ncbi.nlm.nih.gov
 Abstract The international DNA sequence databases abound in fungal sequences not
annotated beyond the kingdom level, typically bearing names such as “uncultured fungus” …

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

B Robbertse, PK Strope, P Chaverri, R Gazis… - Database, 2017 - academic.oup.com
The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National
Center for Biotechnology Information (NCBI) is dedicated to the clear association between …

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

RH Nilsson, AFS Taylor, RI Adams, C Baschien… - …, 2018 - pmc.ncbi.nlm.nih.gov
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 …

What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed …

AB Siddique, AM Khokon, M Unterseher - MycoKeys, 2017 - diva-portal.org
Comparative simultaneous studies of environmental high-throughput sequencing (HTS) and
cultivation of plant-associated fungi have rarely been conducted in the past years. For the …

Dnabarcoder: An open‐source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification

D Vu, RH Nilsson, GJM Verkley - Molecular Ecology Resources, 2022 - Wiley Online Library
The accuracy and precision of fungal molecular identification and classification are
challenging, particularly in environmental metabarcoding approaches as these often trade …

Aspergillus subgenus Polypaecilum from the built environment

JB Tanney, CM Visagie, N Yilmaz… - Studies in …, 2017 - ingentaconnect.com
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In
this study, we employed a combined culture-independent (454-pyrosequencing) and culture …