Mycobiome of the external ear canal of healthy cows

The yeasts of the genus Malassezia belong to the normal skin microbiota of a wide range of warm-blooded animals. In cows, different species of the genus have been isolated such as M. equina, M. nana, M, furfur, M. slooffiae and M. pachydermatis. However, the significance of these yeasts in cows is practically unknown. In the present study the mycobiota of the external ear canal of healthy cows was assessed by cytology, culture, PCR and next generation sequencing (NGS). Even though no growth was obtained in any of the cultured plates, the presence of two cell morphologies typically of Malassezia was determined by cytology in half of the samples. Also, the presence of Malassezia was detected in more than half of the samples by PCR amplification of a highly conserved region within the 5.8S ribosomal RNA of Malassezia. A selection of the samples was analyzed by NGS using the LSU as target gene. The metagenomic analysis revealed that Ascomycota was the predominant phylum followed by Basidiomycota. However, M. pachydermatis was the main species in the external ear canal of healthy cows. Also, the Malassezia phylotype 131 was detected in low abundance in the samples. Nor M. nana nor M. equina sequences were detected in the samples. This is the first attempt to study the external ear canal of healthy cows using advanced molecular methods as NGS.