On the Path from Description to Pathogenesis: Investigation of the Cutaneous Fungal Microbiota in Healthy and Allergic Companion Animals

Next-generation sequencing (NGS) of host-associated microbes has revolutionized our understanding of commensal microbiota diversity and their interaction with the host to influence health and disease. The purpose of this work was at first descriptive, to undertake the founding studies using NGS to describe the cutaneous fungal microbiota (mycobiota) of dogs and cats, and to investigate alterations in allergic animals. The final study investigated the species level distribution and temporality of one fungal commensal, Malassezia, owing to its role in secondary yeast dermatitis of allergic dogs. A greater diversity of fungi was sequenced from skin swabs than was previously described using culture-dependent methods. The cutaneous mycobiota was predominated by environmental fungi and was more diverse on haired body sites than mucosal sites. The skin of allergic dogs harbored fewer types of fungi compared to healthy controls and a fungal dysbiosis was identified in allergic dogs and cats. Further analysis revealed a species level dysbiosis of Malassezia with significantly more M. restricta and M. globosa on the healthy canine skin, and M. pachydermatis on allergic skin. M. pachydermatis was 8-fold more abundant on the skin of laboratory atopic dogs prior to allergen exposure. These findings raised new questions regarding the cause of fungal dysbiosis. Some proposed explanations include immunologic dysfunction in the allergic individual or alterations to the skin barrier functions including hydration and nutrient availability, especially triglycerides and ceramides for Malassezia. Future studies with greater numbers of animals, as well as simultaneous investigations of immune function, skin morphology, and skin lipidomics might provide insights into the pathogenesis of fungal dysbiosis and secondary yeast in in allergic animals