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Abstract

Emerging from the shadows of the numerically superior bacterial microbiome, fungi - comprising 0.1 – 2 % of the microorganisms inhabiting our body - are rapidly gaining recognition for their significant impacts on their surroundings. These commensal fungi, referred to as the mycobiome, reside mainly in the gut but can also be detected in other niches of the body. They interact with their environment, namely the surrounding bacteria and their host in many ways, by secreting metabolites, cross talking with the immune system, or breaching the intestinal barrier and shifting into an infectious state under specific conditions. Research on commensal fungi has only recently come into focus and suggested important roles for them, with shifts in their community composition associated with many different diseases. As mechanistic studies are still largely lacking, further research is required to understand the complex interactions between fungi and host to untangle causative connections. To investigate the interplay between commensal fungi and their mammalian host I established and characterized various set-ups with increasing complexity. I focused on five commensal fungi species that are frequently detected in stool sequencing studies: Candida albicans, Candida tropicalis, Saccharomyces cerevisiae, Malassezia globosa, and Malassezia restricta. By characterizing their growth behavior and metabolite production in vitro, I determined key differences between individual species. Exposure of human intestinal organoids to fungal supernatants did not reveal direct effects on organoid growth or DNA damage. Therefore, I established a fungi-organoid coculture system to model live fungi-host epithelium interaction, which also allows the study of intracellular fungi. While it was possible to detect these, the coculture set-up appeared to be a more accurate representation of an infectious disease setting rather than a commensal one, potentially due to the lack of an immune system. To model a commensal state, I thus turned to mouse colonization models, after adapting different fungi detection methods. Two of the fungi successfully colonized the intestine of mice without causing systemic infection with varying degrees of background microbiomes. I characterized the colonization through transcriptomics of the intestinal mucosa and serum metabolomics, where I could detect species-specific fungal signatures. Additionally, I determined that ex-germ-free mice outside the germ-free facility acquire a natural microbiome that not only caused fungal colonization resistance, but also heavily influenced the transcriptomic and metabolomic output. This was similar in antibiotics-treated mice. Therefore, to characterize the isolated fungi signal while ruling out several confounding factors, I inoculated isolator-housed germ-free mice with a single fungi species. Furthermore, I calibrated an acetaminophen-induced acute liver failure model to show that intestinal C. albicans colonization on its own could reduce liver damage, while C. albicans-driven assembly of a bacterial community exacerbated it. In addition to that, C. albicans colonization could exert a systemic effect on its host in a breast cancer mouse model by lightening the tumor burden. At the same time, the fungi colonization appeared to increase the metastasis rate, which was potentially mediated via the secretion of serum metabolites. Overall, I could identify several new axis of interaction between commensal fungi and their mammalian host, which influenced progression of two different diseases.