Ambystoma maculatum skin microbiomes during Bd infection
Global spread of animal pathogens has contributed to species declines and extinctions. In regions where a particular disease is enzootic, pathogen inhibition may arise through protection provided by host-associated microbiomes. Amphibians skin microbiomes can inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd), preventing emergence of disease through microbe production of anti-fungal secondary metabolites, allowing hosts to resist Bd infection. However, it remains unclear how skin microbiomes may shift in community composition or structure following Bd infection, and whether such shifts differ across Bd strain types. We assessed infection dynamics of Bd-resistant amphibians (Ambystoma maculatum) following experimental exposure to enzootic and epizootic strains of Bd-GPL and tracking pathogen load and bacterial skin microbiome community responses from exposure through to recovery, using 16S rRNA metabarcoding. We found that microbiome communities shifted post-exposure, with increasing diversity, dominance, abundance, and total proportion of known Bd-inhibitory microbes, indicating microbial rescue effects during infection. We also observed lower intra-host variation in diversity during recovery, indicating a shared functional response across the host population and broadly indicative of microbial community resilience. Salamanders exposed to enzootic Bd had greater pathogen loads over time and demonstrated more prolonged community changes and more protective microbiomes, whereas epizootic Bd infection was more rapidly cleared following temporary increase in inhibitory microbes. Collectively, these results indicate that skin microbiomes offer a crucial barrier to fungal disease in Bd-resistant amphibians, with exposure to pathogens inducing changes in microbial community structure that benefit hosts, possibly driven by localized coevolutionary changes in infection dynamics. Our work illustrates how complex host-pathogen interactions are mediated by skin microbiomes through changes in microbial community dynamics that favor pathogen resistant organisms.