Delving further than "skin deep" into the vertebrate skin microbiome

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It is an exciting time for microbiologists who study the skin microbiome! High-throughput sample processing and bioinformatics workflows allow researchers to use simple swabs to collect and analyze the many microbial species that inhabit the skin, including bacteria, archaea, viruses, and fungi. Identifying these microorganisms, their roles, and factors that shape skin microbial communities offers enormous potential for applications related to the treatment of disease, development of probiotics and skin care, and discovery of potentially novel conservation options for endangered species.

The curiosity-driven research of Ashley Ross (undergraduate student, then MSc student in the Neufeld lab) skin microbiome began five years ago when she began studying the microbial biogeography of door handles across the University of Waterloo campus. Unsurprisingly, these surfaces were covered in skin bacteria from the multitude of campus dwellers and we were able to see patterns related to building usage. One experiment led to another, and we became intrigued by the skin microbiome of both humans and animals. Channeling the spirit of innovation of the University of Waterloo, we embarked on an extensive sampling effort to collect as many human and non-human animal skin swab samples that we could in Southwestern Ontario. In partnership with the Toronto Zoo, the African-Lion Safari, the Kitchener Waterloo Humane Society, the University of Guelph, and numerous farms and pet owners, we collected hundreds of mammalian skin swabs from 38 species. Key findings of this work indicated that co-habiting human partners can be linked via their skin microbiomes, and that parallels exist between mammalian skin microbes and host evolutionary histories.

Although many other microbiologists have swabbed and characterized microbes on skin from a plethora of animals around the world, we noticed that existing skin microbiome literature reviews focused primarily on humans. To help us better explore the broader vertebrate literature context of our work, we partnered with Aline Rodrigues Hoffmann (Texas A&M University) to summarize current knowledge related to the vertebrate skin microbiome. This collaborative review helped us appreciate that, despite extensive biological differences in skin composition among diverse vertebrate species, general trends were nonetheless apparent. For example, host species and geographic location are important for shaping skin microbiome composition. In addition, the external placement of this organ results in the presence of commensals that are transferred maternally, as well as other microbes immigrating via contact with soil, air, or water. Other factors that influence skin microbial communities among vertebrates include the biological sex of the host and whether the animal is in captivity or cohabiting with other animals of the same or different species.

Overall, we believe that synthesizing these trends in our review will help establish a strong basis for researchers that continually seek to explore exciting and timely new research directions within the context of the skin microbiome. For example, our review draws attention to a paucity of high-throughput sequencing studies conducted on reptile skin, despite these animals being afflicted with numerous and often-fatal skin diseases. In addition, amphibians are currently being decimated by chytrid fungi. Conservationists urgently need more tools for preventing the spread of this skin disease. Novel probiotics composed of microorganisms that resist the establishment of fungal infections could potentially improve the outlook for these animals. Probiotics also have the potential to help address other skin diseases that affect humans and other animals. For all of these reasons, we are excited to offer this review as a state-of-knowledge that can assist microbiome scientists as we delve further than "skin deep" into the vertebrate skin microbiome.

Ashley Ross

PhD Candidate, University of Guelph