Research Article: Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

Date Published: November 5, 2015

Publisher: Public Library of Science

Author(s): Guangxi Wu, He Zhao, Chenhao Li, Menaka Priyadarsani Rajapakse, Wing Cheong Wong, Jun Xu, Charles W. Saunders, Nancy L. Reeder, Raymond A. Reilman, Annika Scheynius, Sheng Sun, Blake Robert Billmyre, Wenjun Li, Anna Floyd Averette, Piotr Mieczkowski, Joseph Heitman, Bart Theelen, Markus S. Schröder, Paola Florez De Sessions, Geraldine Butler, Sebastian Maurer-Stroh, Teun Boekhout, Niranjan Nagarajan, Thomas L. Dawson, Gregory S. Barsh

Abstract: Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.

Partial Text: Over 100 years ago Malassezia was recognized as an inhabitant of human skin and implicated in a common skin disorder i.e. seborrheic dermatitis [1]. Since then, Malassezia has been found on the skin of all tested warm blooded animals [2,3], including dogs, horses, pigs, goats, cats and lambs [4–8], and associated with other common skin disorders including dandruff [9], atopic eczema/dermatitis, pityriasis versicolor, seborrheic dermatitis, and in systemic disease [10]. Recent investigations of the skin microbiome using culture-free approaches have highlighted the overwhelming dominance of Malassezia among eukaryotes on all human surface body sites, with only the exception of three foot sites [11,12]. Other studies have suggested that they are abundant in body sites beyond skin, including the human oral microbiome [13], but a systematic characterization of Malassezia species and their functional repertoires represented in metagenomic datasets has been hampered by the lack of reference genomes (only 2 out of 14 known species have reference genomes i.e. M. globosa [2] and M. sympodialis [14]). In addition, several reports have suggested that Malassezia-like organisms are found in a wide range of environmental habitats, from deep sea sediments, hydrothermal vents and arctic soils, to marine sponges, stony corals, eels, lobster larvae, and nematodes [15]. These studies have relied on high-identity DNA sequence matches to short amplified barcode regions, but concerns about amplification bias or laboratory contamination raise doubts about the results and the lack of a comprehensive genus-wide genomic resource for known species has made it challenging to investigate this question further.

Malassezia, while found on all humans and associated with many common human skin diseases, are poorly understood in large part due to a lack of genomic tools. Here, we report generation and analysis of the genomes of all 14 accepted Malassezia species, including multiple strains of those most commonly found on human skin (for a total of 24 strains). Malassezia are unique in several ways, including their adaptation to life on animal skin, their dominance as eukaryotic residents on human skin (in contrast to the diversity seen among prokaryotic commensals), and their lipid-dependent lifestyle. Even within Malassezia, we noted there is substantial variability in preference for food sources and thus environmental niches. As a first step, the analysis in this study serves to systematically catalog and characterize genomic features unique to Malassezia and its lineages, which could then be associated with the observed phenotypes. This was aided by the characterization of all known species in the genus as well as multiple strains for key species, allowing robust conclusions to be drawn despite potential analysis pitfalls. Correspondingly, several of the genes identified in this study are prime candidates for further experimental study. It is tempting to speculate, for example, that the gene containing the PFam family PF06742 serves an essential function in Malassezia such that loss of the gene could be lethal. As this gene was likely horizontally acquired by the ancestor of all Malassezia, its function could also be tied to the origin of the genus, particularly if it relates to utilizing energy sources from the host. Similarly, the role of PF13367 could be linked to the ability of cluster B Malassezia to thrive on human skin. In general, Malassezia are not facile experimental systems as they are challenging to cultivate and typically recalcitrant to genetic manipulation. In this context, recent success in performing gene deletion in M. furfur is encouraging (Giuseppe Ianiri and Alexander Idnurm, personal communication) and could enable in vivo functional characterization.