20-BBSRC/NSF-BIO: The amphibian skin microbial-immune interface and its impact on infection outcome

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. Accumulating evidence indicates that immune systems establish intimate relationships with these microbiomes, which may make the difference between life and death for an animal exposed to a pathogen. Amphibians exemplify the importance of studying interactions among microbiomes, immune systems and pathogens. Amphibians across the globe are dying from infection by the chytrid fungus Batrachochytrium dendrobatidis (Bd). Bd infects the skin of amphibians and causes death by disruption of essential skin function. Amphibian skin microbiome and immune system components have been shown to independently relate to Bd infection outcomes. Yet, the interactions among host microbiomes, host immune systems and the pathogen Bd remain poorly understood. This microbial-immune interface is likely critical to determining Bd infection outcomes. The proposed research is unique and innovative because the investigators will combine laboratory experiments using three 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. They expect to demonstrate that amphibian skin microbiomes and host immune responses are interconnected, multi-facetted systems rather than discrete host and microbial entities.

The central hypothesis guiding the proposed studies is that the interdependence of amphibian skin microbiomes and resident immune cell populations critically define Bd infection outcomes. The interdisciplinary research team will integrate microbial ecology, comparative immunology, meta-transcriptomics and proteomics at multiple experimental scales. They will combine these comprehensive system-level datasets with network analyses and structural equation modeling to examine the amphibian skin microbial-immune interface and its effect on amphibian susceptibility to the disease chytridiomycosis, caused by Bd infection. They will address their hypothesis by: 1) determining how skin microbiomes affect skin immune cell populations, 2) defining how skin-resident immune cells affect skin microbiomes, 3) resolving the contribution of the microbial-immune interface in Bd infection outcomes. They predict that key microbial-immune interactions strongly impact Bd susceptibility. Their findings will garner the much-needed understanding of the microbial-immune interface and how these interactions impact disease outcomes. Theirs will be the first study to simultaneously evaluate the relative contribution of the microbiome and immune system to chytridiomycosis in a causal framework. Vertebrate animals, including humans, are host to symbiotic microbes and complex immune system components. The resulting insight from these investigations will have broad applicability to a variety of other animal systems.

Understanding how host microbiomes and immune systems interact and respond to invading pathogens is of broad theoretical and applied interest. We have assembled a multidisciplinary research team that will combine our respective expertise in microbiome biology, innate immunity, meta-transcriptomics, proteomics and multivariate statistics to examine the amphibian skin microbial-immune interface and its effect on host susceptibility to the disease chytridiomycosis, caused by the deadly chytrid fungus Batrachochytrium dendrobatidis (Bd). The amphibian chytrid system is an exceptional model for studying dynamics of host, microbiome and pathogen because we can manipulate the immune system, microbiome and Bd infection status in controlled laboratory experiments with amphibian species that represent the spectrum of Bd susceptibility. Our preliminary findings indicate that bacterial composition of amphibian skin are integrally linked with their skin immune components and impact susceptibility to Bd infection. Accordingly, the central hypothesis guiding our proposed studies is that amphibian skin microbiomes and resident immune cell populations are interdependent and critically define Bd infection outcomes. We will address our hypothesis using experimental manipulations in three amphibian species through the following objectives: 1) determine how skin microbiomes affect skin immune composition and function, 2) define how skin-resident immune cells affect skin microbiome composition and function, 3) resolve the contribution of the microbial-immune interface in Bd infections. We will use cutting-edge molecular, genomic and proteomic approaches at multiple experimental scales, and combine these comprehensive system-level datasets with network analyses and structural equation modeling to identify mechanisms that underlie responses among interacting host microbiomes, host immune systems, and pathogen in skin symbioses and disease.