The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome is strongly associated with disease outcome for several host-pathogen systems, yet its role in Bsal infection remains unresolved. In addition, many in-vivo Bsal studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterised the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt (Lissotriton vulgaris) and the great-crested newt (Triturus cristatus). Bsal infection and subsequent mortality in both newt species was associated with perturbation of the skin microbiome and possible dysbiosis. In addition, reduced microbial diversity and changes in microbiome structure accompanied the transition of newts from the wild to captivity, suggesting a possible decline in microbe-associated protection and increased risk of infection by opportunistic pathogens. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.

Captivity and exposure to the emerging fungal pathogen Batrachochytrium salamandrivorans are linked to perturbation and dysbiosis of the amphibian skin microbiome