Characterization of the Healthy Ocular Mycobiome of Purebred Lusitano Horses Using Oxford Nanopore Long-Read Sequencing

The ocular surface represents a unique microbial ecosystem continuously exposed to environmental microorganisms; however, the fungal component of the healthy equine ocular microbiome remains poorly characterized. This study aimed to characterize the ocular surface mycobiome of 12 clinically healthy Purebred Lusitano horses from three geographical regions in Portugal kept in two housing systems using Oxford Nanopore long-read sequencing and conventional fungal culture. Sequencing revealed a highly diverse fungal community with marked inter-individual variability. The most abundant genera were Wallemia, Podosphaera, Debaromyces, Aspergillus, Filobasidium, Kurtzmaniella, Metschnikowia, Malassezia and Spathaspora. Patterns of fungal community composition suggested that local environmental conditions may contribute to the observed inter-individual variability. Genera commonly associated with equine fungal keratitis, including Aspergillus, Fusarium and Penicillium, were detected in healthy horses irrespective of housing system. Overall, the healthy equine ocular surface was characterized by a diverse mycobiome dominated by environmentally associated fungi. There findings provide a baseline for future studies investigating ocular microbial dysbiosis, environmental determinants of fungal community structure, and equine ocular health.