ABSTRACT
The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S), and to improve the taxonomy assignment of the communities in real-time and up to the species level. We assess amplicons targeting a 3.5 Kb region (V3 18S-ITS1-5.8S-ITS2-28S D2) and a 6 Kb region (V1 18S-ITS1-5.8S-ITS2-28S D12) with the What’s in my pot (WIMP) classifier. We used the ZymoBIOMICS™ mock community and different fungal cultures as positive controls. Long amplicon sequencing correctly identified Saccharomyces cerevisiae and Cryptococcus neoformans from the mock community, as well as Malassezia pachydermatis, Microsporum canis, Aspergillus fumigatus from the microbiological cultures, and identified Rhodotorula graminis as the species mislabelled as Candida spp in the previous culture.
We applied the same approach to communities, such as external otitis in dogs. Malassezia spp was found as the dominant fungi in the ear skin. We identified M. pachydermatis as the main species in the healthy sample, and a higher representation of M. globosa and M. sympodialis in otitis affected samples. We demonstrate the suitability of this approach to characterize the fungal community of complex samples, either healthy samples or samples with clinical signs of infection.