Global atlas of fungi – the GlobalFungi Database

The advent of molecular methods resulted in an enormous growth of reports on microbial communities from various habitats, but the scattered information is difficult to access. The GlobalFungi database (https://globalfungi.com) offers FAIR access to data from published sources.

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Thanks to the recent advance of high-throughput-sequencing methods we are facing an accumulating wealth of fungal sequencing data from various geographical regions, ecosystems and habitats. Although the application of NGS methods revolutionized our understanding of fungal ecology, the accumulating raw fungal NGS data in sequence repositories did not bring much extra value so far. The idea behind the GlobalFungi Database (https://globalfungi.com) is to establish a platform that provides the access to published data on fungal community composition obtained by next-generation-sequencing through to everyone through a web based interface that allows various queries and visualization of the results. This idea was conceived by a group of researchers from the Institute of Microbiology of the Czech Academy of Sciences in Prague – the GlobalFungi team and should support the FAIR Data Principles: make data Findable, Accessible, Interoperable and Reusable and provide a convenient access for users.

Front page of the GlobalFungi Database. Figure credits: The GlobalFungi Team

 

The database covers data from all terrestrial habitats except those subject to experimental manipulation, containing information on fungal communities from soil, litter, dead plant material, living plant tissues and others. At present, the database contains over 650 millions of observations of individual fungal taxa in the form of DNA sequences that were detected in one of 20 000 samples collected from more than 200 published studies.

The user interface at https://globalfungi.com enables the users to access the database in several ways. In the taxon search, it is possible to search for genera and species of fungi or for the molecular taxa “species hypotheses”, to visualize the geographic distribution and abundance of each taxon and to retrieve sequences as well as environmental metadata.

The genus Fusarium contains important pathogens of several agricultural crops and represents a threat to the future food security. The understanding of its distribution and the environmental and climatic factors that affect it may help to minimize its negative impacts. Figure credits: Miroslav Kolarik and the GlobalFungi Database (https://globalfungi.com).

 

The sequence search allows to search the sequence database by DNA similarity either by exact match on based on a similarity threshold. It is also possible to open individual studies and access their content. In the geosearch, users can select a group of samples on the map and analyse the local fungal flora.

Importantly, the database is a steadily growing resource maintained by the GlobalFungi Team. Because the authors believe that sharing is important, authors of new papers are encouraged to submit their data and make their results visible to the public. The database webpage guides the submitters through an interactive process allowing them to upload sequencing data and metadata.

Fungi are essential as plant symbionts that allow wild plants as well as agricultural crops to get access to soil nutrients but also represent important pathogens of plants and animals that may negatively affect health of ecosystems or food security. Each individual study on fungi represents a piece towards the understanding of the ecology of this important group of organisms, but sharing the accumulated information gives the funding invested into the exploration of fungi an additional value. The GlobalFungi Database should be the interface for such data valorization.

Read the full paper here:

https://www.nature.com/articles/s41597-020-0567-7

Petr Baldrian

Group Leader, Institute of Microbiology of the Czech Academy of Sciences

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