Host-associated microbes form an important component of immunity that protect
against infection by pathogens. Treating wild individuals with these protective microbes,
known as probiotics, can reduce rates of infection and disease in both wild and captive
settings. However, the utility of probiotics for tackling wildlife disease requires that
they offer consistent protection across the broad genomic variation of the pathogen
that hosts can encounter in natural settings. Here we develop multi-isolate probiotic
consortia with the aim of effecting broad-spectrum inhibition of growth of the lethal
amphibian pathogen Batrachochytrium dendrobatidis (Bd) when tested against nine
Bd isolates from two distinct lineages. Though we achieved strong growth inhibition
between 70 and 100% for seven Bd isolates, two isolates appeared consistently
resistant to inhibition, irrespective of probiotic strategy employed. We found no evidence
that genomic relatedness of the chytrid predicted similarity of inhibition scores, nor that
increasing the genetic diversity of the bacterial consortia could offer stronger inhibition
of pathogen growth, even for the two resistant isolates. Our findings have important
consequences for the application of probiotics to mitigate wildlife diseases in the face of
extensive pathogen genomic variation
