The immune system is one of the primary ways animals fight pathogenic microorganisms. Animals also live with millions of non-pathogenic microorganisms (their microbiomes) which cause them no harm. Emerging evidence shows that immune systems form intimate relationships with these microorganisms, potentially making the difference between life and death for an animal exposed to a pathogen. Amphibians, hundreds of species of which are threatened by the deadly chytrid fungus Batrachochytrium dendrobatidis (Bd), highlight the importance of these interactions. Bd infects the skin of amphibians and causes death by disruption of essential skin function. Amphibian skin microbiome and immune system components independently affect Bd infection outcomes but the complex three-way interaction between disease, microbiome and immune system remain poorly understood. Our research combines laboratory experiments using amphibian species that differ in Bd susceptibility with state-of-the-art molecular and analytical approaches. Together, they aim to define the mechanisms controlling the microbial-immune interface and its effect on Bd susceptibility, demonstrating that amphibian skin microbiomes and host immune responses are interconnected, multi-facetted systems rather than discrete host and microbial entities.
A second component of this work aims to understand the eco-evolutionary processes shaping amphibian-associated microbial communities, which may have significant practical implications for biodiversity conservation. Combining experimental microbiology and genomic approaches, we investigate how interactions among bacterial species living on amphibian skin influence microbiome assembly and how these interactions may shift under future climate scenarios. We also use genome sequencing to uncover the metabolic functions of microbes, including how they can inhibit Bd. These approaches help us better understand the roles amphibian skin bacteria play in chytrid resistance.
The emerging field of wildlife probiotics has the potential to effectively mitigate wildlife outbreaks. For these interventions to be effective, however, the introduced probiotics need to persist, and this is likely to depend on the host-microbiome-environment interactions that play out in wild settings. Therefore, understanding the dynamics of host-associated microbiome specificity and host-microbe co-evolution is crucial for designing effective microbiome-manipulation strategies to combat pathogen-mediated biodiversity loss.