Adding Complexity to Models of Candida albicans Human Colonization: Natural Isolates and Polymicrobial Interactions

Abstract

The fungus Candida albicans represents a commensal colonizer of human mucosal surfaces and an opportunistic pathogen capable of causing both superficial mucosal and life-threatening disseminated infections. C. albicans is remarkably versatile and readily adapts to diverse environment conditions, allowing it to colonize multiple host niches. To adapt to changing environmental conditions, C. albicans may undergo a morphological transition, alters its metabolism, or actively remodel its multilayered cell wall. As life-threatening invasive infections arise from populations already colonizing the gastrointestinal tract, it is important to characterize C. albicans' role as both a commensal and pathogen, to inform how the shift to pathogenesis occurs. The majority of research in C. albicans has been performed in the standard reference strain, SC5314, but C. albicans isolates display incredible genotypic and phenotypic diversity that can be leveraged to uncover new facets of fungal biology. We collected over 900 commensal C. albicans isolates from healthy donors to characterize within-host diversity and identify adaptations associated with commensalism. We demonstrated that healthy people can be simultaneously colonized by multiple, distinct lineages of C. albicans. These commensal isolates displayed wide variation in their phenotypic properties but consistently retained their ability to filament, a trait that is often associated with pathogenicity. Importantly, despite originating from healthy donors, all our commensal isolates maintained a high pathogenic potential. We did not identify any phenotypes that separated isolates by sample site or genetic clade, emphasizing the highly adaptive nature of C. albicans. Finally, we demonstrated that closely related isolates with divergent phenotypes can be leveraged to identify causative mutations through comparative genomics. This work emphasizes the versatility of C. albicans and highlights the value of characterizing natural diversity. The fungal cell wall is an essential organelle that mediates interactions with host immune cells and represents a major target of antifungals. Due to its important roles, the fungal cell wall is highly responsive to its environment and undergoes active remodeling in response to changing environmental conditions. Alterations in cell wall composition can allow C. albicans to evade immune detection or better tolerate antifungal drugs. Although bacteria are known to have profound impacts on fungal biology and virulence, little work has investigated how bacteria may influence the fungal cell wall and any downstream consequences on fungal virulence. We determined that bacterial co-culture induces cell wall remodeling in multiple genetic backgrounds of C. albicans, as well as some related Candida species. Critically, bacterial-mediated fungal cell wall remodeling alters antifungal sensitivity and immune recognition of C. albicans. We demonstrate that this interaction is relevant in vivo, as the addition of a single bacterial species to C. albicans colonizing the murine gastrointestinal tract was sufficient to change the cell wall. These findings underscore the importance of considering bacterial influences on C. albicans biology and virulence. Overall, this dissertation demonstrates the power of incorporating host-relevant conditions when conducting research. Characterizing natural isolates of C. albicans, both commensal and clinical, from human hosts provides deeper insight into fundamental aspects of fungal biology. Considering the impact of and including bacteria in models of C. albicans colonization and disease increases the relevancy of our experimental results and more accurately replicates the reality of human colonization and disease. Ultimately, carefully incorporating further complexity in our studies improves our understanding of the intricate relationships between fungus and host.