Han, G.; Yunker, R.; Hasan, M. H.; Bruce, A.; Baldaro, K.; Pacia, J.; Lockwood, O.; Miralles, D. M.; Jarjour, N. N.; Chellappa, K.; Vaishnava, S.; Beura, L. K.

Throughout evolution, organisms have developed exclusive and mutually beneficial relationships with microbes in their natural environments. While these species-specific host-microbe interactions are well-documented for in case of commensal bacteria, similar relationships for commensal fungi remain largely unexplored. In this study, we screened the gut mycobiome of non-laboratory rodents, to find host-specific fungi. We identified Kazachstania pintolopesii as a dominant fungus in pet store mice across various geographical locations. This fungus stably colonized laboratory mice, outcompeted non-murine fungi, and persisted independently of gut bacteria without triggering conventional antifungal responses. Colonization by K. pintolopesii significantly increased intestinal macrophage populations, which was crucial in preventing systemic immune recognition. K. pintolopesii also induced intestinal type 2 immune responses, providing cross-kingdom protection against helminths in free-living mammals exposed to parasitic protozoa. Notably, K. pintolopesii strains from non-murine hosts failed to colonize laboratory mice with intact gut bacteria despite high genomic similarity. In gnotobiotic mice, these non-murine strains disrupted bacterial communities and their associated metabolomes, unlike the mouse strains. Our findings establish host exclusivity as a hallmark of fungal commensalism and reveal commensal bacteria as gatekeepers of species-specific fungal colonization and their immune interactions with the mammalian host.