White-nose syndrome restructures bat skin microbiomes

Abstract

Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases. Instead of single organisms being associated with disease, community characteristics may be more relevant. Longitudinal microbiome studies of the same individual bats as pathogens arrive and infect a population are the ideal experiment but remain logistically challenging; therefore, investigations like our approach that are able to correlate invasive pathogens to alterations within a microbiome may be the next best alternative. The results of this study potentially suggest that microbiome-host interactions may determine the likelihood of infection. However, the contrasting relationship between Pd and the bacterial microbiomes of Myotis lucifugus and Perimyotis subflavus indicate that we are just beginning to understand how the bat microbiome interacts with a fungal invader such as Pd.

Keywords: Eptesicus fuscus; Myotis lucifugus; Perimyotis subflavus; Pseudogymnoascus destructans; bat populations; disease ecology; microbiome; white-nose syndrome.

Fig 1

Bat sample collection distribution map. E. fuscus samples were collected from seven hibernacula 2011–2015. M. lucifugus samples were collected from 20 hibernacula 2011–2016. P. subflavus samples were collected from 13 hibernacula 2011–2016.

Fig 2

Bacterial and fungal microbiome taxonomy characterization. Bacterial characterization at the order level showed that for E. fuscus (A1) 66.5% of the bacterial OTUs were assigned to the order Pseudomonadales, for M. lucifugus (B1), Enterobacteriales was the most abundant bacterial order with 15.4% of the bacterial OTUs, and Pseudomonadales was the most abundant bacterial order for P. subflavus (C1) with 20.9% of the bacterial OTUs. Fungal microbiome characterization at the order level showed that for all three bat species, Saccharomycetales was the most abundant fungal order; however, it’s abundance varied significantly between each species (E. fuscus, 25.6%; M. lucifugus, 49.4%; P. subflavus, 79.2%).

Fig 3

Measures of bacterial and fungal evenness, richness, and Shannon indices between Pd-positive and Pd-negative bats. There were no significant differences when comparing (A1) bacterial or (B1) fungal diversity between Pd-positive and Pd-negative E. fuscus. (A2) Bacterial diversity comparisons in M. lucifugus found the evenness, richness, and Shannon diversity were all significantly higher in Pd-negative bats. (B2) Fungal diversity comparisons in M. lucifugus did not indicate any difference between Pd-positive and Pd-negative bats. (A3) There were no significant differences when comparing bacterial diversity between Pd-positive and Pd-negative P. subflavus; however, (B3) fungal diversity results from P. subflavus indicate that Pd-positive bats have a higher fungal evenness and Shannon diversity.

Fig 4

Relative abundances of bacterial epidermal communities of Pd-positive and Pd-negative M. lucifugus. Measures of relative abundance between the bacterial epidermal communities from swabs taken from Pd-positive and Pd-negative M. lucifugus revealed an overabundance of the bacterial family Pseudonocardiaceae in Pd-positive bats, while unaffected bats showed an overabundance of bacterial families Brucellaceae, Cytophagaceae, and Rhizobiaceae, as well as the bacterial order Chromatiales.

Fig 5

Bacterial (A) and fungal (B) differences between bat epidermal and substrate microbiome composition. Bacterial results indicate a significant difference in diversity between bat and substrate samples, with substrate samples containing a higher Shannon diversity. Fungal results did not indicate a significant difference in diversity between bat and substrate samples.