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Mycobiome diversity: high-throughput sequencing and identification of fungi.

Review article
Authors R. Henrik Nilsson
Sten Anslan
Mohammad Bahram
Christian Wurzbacher
Petr Baldrian
Leho Tedersoo
Published in Nature reviews. Microbiology
Volume 17
Pages 95-109
ISSN 1740-1534
Publication year 2019
Published at Department of Biological and Environmental Sciences
Pages 95-109
Language en
Keywords Fungi ; ecology ; nutrient cycling ; climate change ; systematics ; high-throughput sequencing ; review
Subject categories Nano Technology, Agricultural Science, Forestry and Fisheries, Veterinary Science, Software Engineering, Databases, Data processing, Bioinformatics (Computational Biology), Climate Research, Environmental Sciences, Oceanography, Microbiology, Botany, Zoology, Bioinformatics and Systems Biology, Genetics, Ecology, Biological Systematics, Terrestrial ecology, Freshwater ecology, Marine ecology, Evolutionary Biology, Functional genomics, Medical microbiology


Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.

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