Exploiting symbiosis to identify novel antifungals to combat emerging drug-resistant pathogens

High levels of drug resistance is a defining feature of the emerging pathogen Candida auris and this is associated with high levels of attributable mortality in ongoing hospital outbreaks, thus necessitating the discovery of new antifungals. Bacteria are a potent source of antifungals, however, traditional routes for antifungal discovery from bacterial natural products often result in either the rediscovery of known antifungals or identification of molecules with high host toxicity. To counteract these hurdles, we propose that focusing on symbiotic bacteria, i.e., those that are able to co-exist with and provide benefit to their eukaryotic hosts, will be more likely to result in discovery of potent antifungal molecules with low mammalian host toxicity. This application details experiments to address a fundamentally and clinically important gap in the identification and development of much-needed antifungals. In our previous work, we identified potent antifungal molecules from symbiotic bacteria, but their mechanisms of action against drug-resistant C. auris are still unknown. We have expanded our collection of symbiotic bacteria from hosts including squid, tunicates, ants, honeybees, fruit flies, mice, and humans. Many of these beneficial bacteria have co-evolved with their eukaryotic hosts to provide antifungal protection of important resources (e.g., externally gestating eggs, underground fungus gardens, and hives). Antifungal screening of these host-associated bacteria revealed many with potent activity against Candida auris, especially when bacteria were co-cultured with environmentally-relevant fungi to induce metabolite production. Given our extensive symbiotic bacterial library, our suite of previously isolated antifungal molecules, and our fungal genetic tools to identify mechanism of action of new antifungals, we are primed to discover and characterize new, selective antifungal molecules with low host toxicity. In this proposal, we describe our rapid screening platform for novel antifungals that prioritizes activity against resistant fungi, incorporates early understanding of mechanism of action, and deprioritizes samples with mammalian toxicity. Aim 1 focuses on development of a rapid screening platform to induce and characterize novel antifungals from crude and semi-purified extracts of symbiotic bacteria, including our prioritization pipeline for samples with new mechanism and low toxicity. Aim 2 focuses on using yeast genetics approaches to define mechanism of action, starting with existing antifungal molecules from symbiotic bacteria. Together, these studies will advance new concepts for how host-associated bacteria can be exploited and induced to identify potent, selective antifungals with novel mechanism of action that overcome resistance with corresponding low mammalian toxicity, laying a critical foundation for treating this urgent and emerging public health threat. Project Number: 1R21AI197487-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Marcy Balunas (+1 co-PI) | Institution: UNIVERSITY OF MICHIGAN AT ANN ARBOR, ANN ARBOR, MI | Award Amount: $411,078 | Activity Code: R21 | Study Section: Special Emphasis Panel[ZRG1 DCAI-U (02)] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R21AI19748701