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

Nilsson, R. Henrik; Larsson, Karl ­Henrik; Taylor, Andy F. S.; Bengtsson‐Palme, Johan; Jeppesen, Thomas Stjernegaard; Schigel, Dmitry; Kennedy, Peter G.; Picard, Kathryn T.; Glöckner, Frank Oliver; Tedersoo, Leho; Saar, Irja; Kõljalg, Urmas; Abarenkov, Kessy

doi:10.1093/nar/gky1022

Cited by 2,189 publications

(1,215 citation statements)

References 36 publications

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“…In addition, ITSx (Bengtsson‐Palme et al., ) was used to extract ITS sequences from WMS data in order to conduct an ITS‐based taxonomic analysis. Extracted ITS reads were analyzed using default parameters of QIIME (Caporaso et al., ) with closed‐reference clustering for OTU picking with 97% identity and the UNITE database version 7.2 (Nilsson et al., ).…”

Section: Methodsmentioning

confidence: 99%

“…16S rRNA gene amplicon sequencing reads underwent taxonomic assignment using QIIME2 (Bolyen et al, ) which includes vsearch dereplicate‐sequences function for dereplication and q2‐feature‐classifier for taxonomic assignment and the SILVA v128 database (Quast et al., ) while default parameters of QIIME (Caporaso et al., ) with closed‐reference clustering for OTU picking with 97% identity and UNITE database version 7.2 (Nilsson et al., ) were used for ITS amplicon analysis.…”

Section: Methodsmentioning

confidence: 99%

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Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Arıkan

Mitchell

Finn

et al. 2020

Journal of Food Science

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Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Arıkan

Mitchell

Finn

et al. 2020

Journal of Food Science

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“…We evaluated the range extents of OTUs identified from worldwide collections of 12 species‐rich mushroom genera from the UNITE database (Nilsson et al, ). Seven of the genera are ectomycorrhizal ( Amanita , Cortinarius , Hebeloma , Hydnum , Hygrocybe , Inocybe , and Russula/Lactarius ) and five are saprotrophic ( Agaricus , Galerina , Hygrophorus , Lepiota , and Pholiota ).…”

Section: Methodsmentioning

confidence: 99%

Over the hills, but how far away? Estimates of mushroom geographic range extents

Bazzicalupo

Whitton

Berbee

2019

Journal of Biogeography

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Aim Geographic distributions of mushroom species remain poorly understood despite their importance for advancing our understanding of the habitat requirements, species interactions and ecosystem functions of this key group of organisms. Here, we estimate geographic range extents (maximum within‐species geographic distance) of genetically defined operational taxonomic units (OTUs). Location World‐wide, with emphasis on the American Pacific Northwest. Taxa Amanita, Agaricus, Cortinarius, Galerina, Hebeloma, Hydnum, Hygrocybe, Hygrophorus, Inocybe, Lepiota, Pholiota, and Russula + Lactarius; other genera in Agaricomycotina. Method We used publicly available OTUs from ribosomal internal transcribed spacer (ITS) sequences (n = 15,373) from 12 mushroom genera with worldwide distributions. For each of 2,324 ~ species‐level OTUs, we estimated the maximum within‐species range extent based on sample locality records. In parallel, we estimated range extents for species in four tree genera. Contrasting estimates from well‐studied trees allowed us to test for potential biases in our range estimates of less well inventoried mushrooms. Results The median range extents across the 2,324 mushroom OTUs varied from ~ 1,200 to 4,039 km, depending on assumptions. These extents were significantly lower than estimates from permuted or randomized data. Mushroom ranges were comparable to the median natural range extent of tree species (1,613 km). In contrast, the tree median species range increased to 16,581 km when anthropogenic range extensions were included. At least 10 mushroom species were similarly broadly distributed, eight of which have been associated with human activity. Main conclusions Overall, like tree species, mycorrhizal and saprotrophic fungi show evidence of biogeographic structure rather than global distributions. This reconstruction of geographic range extents drew upon investments into ITS barcoding of extensive herbarium collections. Large scale analyses such as ours can yield estimates of fungal geographic range extents that are a prerequisite to a deeper understanding of the diverse roles of fungi in ecosystems.

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“…Sequences were taxonomically classified based on the ITS2 region with a naïve Bayesian classifier implemented in MOTHUR against the UNITE database (Nilsson et al. ) with a minimum bootstrap support of 80%.…”

Section: Methodsmentioning

confidence: 99%

“…Taxonomic affiliation of the fungal sequences was then obtained by querying against the UNITE database (Nilsson et al. ).…”

Section: Methodsmentioning

confidence: 99%

Are traded forest tree seeds a potential source of nonnative pests?

Franić

Prospero

Hartmann

et al. 2019

Ecological Applications

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The international seed trade is considered relatively safe from a phytosanitary point of view and is therefore less regulated than trade in other plants for planting. However, the pests carried by traded seeds are not well known. We assessed insects and fungi in 58 traded seed lots of 11 gymnosperm and angiosperm tree species from North America, Europe, and Asia. Insects were detected by X‐raying and molecular methods. The fungal community was characterized using high‐throughput sequencing (HTS) and by growing fungi on non‐selective agar. About 30% of the seed lots contained insect larvae. Gymnosperms contained mostly hymenopteran (Megastigmus spp.) and dipteran (Cecidomyiidae) larvae, while angiosperms contained lepidopteran (Cydia latiferreana) and coleopteran (Curculio spp.) larvae. HTS indicated the presence of fungi in all seed lots and fungi grew on non‐selective agar from 96% of the seed lots. Fungal abundance and diversity were much higher than insect diversity and abundance, especially in angiosperm seeds. Almost 50% of all fungal exact sequence variants (ESVs) found in angiosperms were potential pathogens, in comparison with around 30% of potentially pathogenic ESVs found in gymnosperms. The results of this study indicate that seeds may pose a greater risk of pest introduction than previously believed or accounted for. A rapid risk assessment suggests that only a small number of species identified in this study is of phytosanitary concern. However, more research is needed to enable better risk assessment, especially to increase knowledge about the potential for transmission of fungi to seedlings and the host range and impact of identified species.

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

Cited by 2,189 publications

References 36 publications

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Over the hills, but how far away? Estimates of mushroom geographic range extents

Are traded forest tree seeds a potential source of nonnative pests?

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