Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

Abstract

The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloudbased dynamic data network platform.

MALDI‐TOF MS‐Based Identification of Melanized Fungi is Faster and Reliable After the Expansion of In‐House Database

“…The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and European Confederation of Medical Mycology (ECMM) recommended histopathology, culture and sequencing for accurate species identification, especially for unusual or newly described pathogens . However, the conventional and molecular (DNA based) methods of diagnosis have several limitations . The conventional methods of fungal identification depend on sporulation, whereas many melanized fungi grow very slowly and never sporulate in artificial media .…”

“…The emergence of molecular techniques (DNA sequencing) has improved the identification of melanized fungi, especially when it is unable to produce spores . Although the molecular techniques transformed the taxonomy and epidemiology of melanized fungi, the major problem with DNA based identification is the limited availability of database and lack of inter‐laboratory concordance . Therefore, molecular characterization can be correlated with phenotypic features for reliable identification and rare fungal species should always be confirmed by DNA sequencing …”

Molecular diagnostics in medical mycology

“…More specific searches, such as searches only against culture collection deposits, can be done using Entrez query syntax in the Entrez query-specific search set. An alternative to the NCBI site are smaller biocurated databases that allow BLAST searches, but which contain verified sequences (see Prakash et al for review 66 ). Consequently, a commercialized system may require a closed, biocurated database that can be established using reference sequences from GenBank or other databases, or by generating their own sequences.…”

The Human Lung Mycobiome in Chronic Respiratory Disease: Limitations of Methods and Our Current Understanding

“…Firstly, database choice is a crucial factor. There are several publicly available databases of fungal sequences, including UNITE and ISHAM Barcoding databases [92]. However, although often curated, they can be incomplete and contain inconsistencies due to taxonomic reassignments.…”