Bat skin microbiome and the association of ecoregion and bat species that impacted isolation of members with bioactivity against Pseudogymnoascus destructans

Abstract

Background Microbiome constituents can serve as a primary defense against vertebrate pathogens. This may be crucial to the protection of North American bats who have been devastated over the last two decades by the fungal pathogen, Pseudogymnoascus destructans (Pd) , which causes white-nose syndrome (WNS). The objectives of this study were to isolate members of the external microbiome of bats post-hibernation in Arizona and New Mexico before the arrival of WNS, to identify those bacteria with bioactivity against Pd , and to determine the variables associated with antifungal strains. Results In this study we isolated 2,936 bacteria from the fur and skin of 314 bats across 12 bat species at 6 sites across New Mexico and Arizona from 2013 to 2016. Selective media were used to promote the isolation of Actinomycetota (2,594 isolates, 88.4%), particularly species of Streptomyces (2,045 isolates, 69.7%) known for their bioactivity. Although Actinomycetota isolation was targeted, this collection includes representatives from Pseudomonadota (Alpha-, Beta -, and Gamma-Proteobacteria ), Bacillota , and Bacteroidota phyla also common to the bat microbiome. A bi-layer challenge assay performed on 1,089 isolates identified 61 bat-associated bacteria with activity against Pd. These results were pooled with efforts by Hamm et al. [ 1 ] to determine what metrics impacted isolation of bacteria that inhibit Pd ( n = 97). Ecoregion and bat species were determinant variables associated with Pd inhibition. Conclusions This study represents, to our best knowledge, the largest culture collection of bacteria from bats’ skin and fur before the impact of WNS. We identified bacteria with antifungal activity against Pd and found significant associations of bioactive strains with bat species and ecoregions.