Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host

The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin
of amphibians, and has caused severe declines and extinctions of
amphibians globally. In this study, we investigate the interaction between
Bd and the bacterial skin microbiome of the endangered Sierra Nevada
yellow-legged frog, Rana sierrae, using both culture-dependent and
culture-independent methods. Samples were collected from two populations
of R. sierrae that likely underwent Bd epizootics in the past, but that
continue to persist with Bd in an enzootic disease state, and we address
the hypothesis that such “persistent” populations are aided by mutualistic
skin microbes. Our 16S rRNA metabarcoding data reveal that the skin
microbiome of highly infected juvenile frogs is characterized by
significantly reduced species richness and evenness, and by strikingly
lower variation between individuals, compared to juveniles and adults with
lower infection levels. Over 90% of DNA sequences from the skin microbiome
of highly infected frogs were derived from bacteria in a single order,
Burkholderiales, compared to just 54% in frogs with lower infection
levels. In a culture-dependent Bd-inhibition assay, the bacterial
metabolites we evaluated all inhibited the growth of Bd. Together, these
results illustrate the disruptive effects of Bd infection on host skin
microbial community structure and dynamics, and suggest possible avenues
for the development of anti-Bd probiotic treatments.