Previously, taxonomic classification of anaerobic fungi mainly relied on the use of the Internal Transcribed Spacer region 1 (ITS1). However, in recent years issues with the use of ITS1 as a taxonomic marker for anaerobic fungi have been revealed. This is primarily due to its size polymorphism and sequence heterogeneity, which can be substantial even within a single anaerobic fungal isolate.
Until 2020, the anaerobic fungi network maintained and regularly updated an ITS1 database, which was based on that previously developed by Koetschan et al (2014). The last version of this database (version 3.5, released February 2020) is still available upon request, but is no longer updated. This is because it is time to move to a more robust taxonomic marker, the D1/D2 region of the large ribosomal subunit (LSU) (i.e. 28S rRNA gene).
LSU Database v 2.0 (Released 19 April 2024)
The D1/D2 region LSU database v1.0 was created based on a published dataset containing both isolates and environmental samples (Hanafy et al, 2020). This database has now been updated to include: (i) the two most recently characterised anaerobic fungal genera (Astrotestudinimyces and Testudinimyces), (ii) the four families now recognised, and (iii) the numerous additional novel genera that were discovered in a large herbivore mycobiome census (i.e., NY1-NY56).
Full Region Database v 2.0 (Released 19 April 2024)
The full region sequences (i.e. ITS1 through to the D1/D2 region of the LSU) generated by Hanafy et al (2020) were also previously used as the basis for a ‘full region’ database. This database has also been recently updated to include the full region sequences from the two latest genera (Astrotestudinimyces and Testudinimyces), and the revised family level annotation. Addition of the novel genera NY1-NY56 was not possible due to full region sequences not being available.
Database Files
Details of the files for the two databases are given in the below table. Each database is comprised of two files: a fasta file and .txt file giving the updated taxonomy for all the sequences in the fasta file. Please note, a D1/D2 LSU alignment file will also be made available in due course.
Please note it is not the intention of the databases to include every available anaerobic fungal sequence. These are ‘gold standard’ reference databases which contain representatives of all currently known anaerobic fungal taxa (for which there is sequence data publically available).
| Database | Version | No. of sequences | Database files |
| AF_LSU | 2.0 | 457 | AGF_LSU_database_v2.fasta AGF_LSU_tax_v2.txt |
| AF_FullRegion | 2.0 | 197 | AGF_Full_region_v2.fasta AGF_Full_region_tax_v2.txt |
All the sequences used in the databases come from publicly available resources, with the source origin (i.e. accession number or equivalent) indicated.
As previously, these databases will be periodically updated as new anaerobic fungal taxa are identified.
The databases are compatible with both Mothur & QIIME. Interested in using the databases with a different bioinformatics pipeline? Please get in touch.
How to acknowledge/cite these databases?
A manuscript is in preparation, the details of which will be made available here in due course. In the meantime, please indicate “The AF_Full_Region/AF_LSU* database version 2.0 was obtained from the Anaerobic Fungi Network (www.anaerobicfungi.org).”
*Please delete as appropriate