Environment and host species shape the skin microbiome of captive neotropical bats.

Virginie Lemieux-Labonté,Nicolas Tromas,François-Joseph Lapointe,B. Jesse Shapiro

doi:10.7717/peerj.2430

Abstract

BackgroundA wide range of microorganisms inhabit animal skin. This microbial community (microbiome) plays an important role in host defense against pathogens and disease. Bats (Chiroptera: Mammalia) are an ecologically and evolutionarily diversified group with a relatively unexplored skin microbiome. The bat skin microbiome could play a role in disease resistance, for example, to white nose syndrome (WNS), an infection which has been devastating North American bat populations. However, fundamental knowledge of the bat skin microbiome is needed before understanding its role in health and disease resistance. Captive neotropical frugivorous bats Artibeus jamaicensis and Carollia perspicillataprovide a simple controlled system in which to characterize the factors shaping the bat microbiome. Here, we aimed to determine the relative importance of habitat and host species on the bat skin microbiome.MethodsWe performed high-throughput 16S rRNA gene sequencing of the skin microbiome of two different bat species living in captivity in two different habitats. In the first habitat, A. jamaicensis and C. perspicillata lived together, while the second habitat contained only A. jamaicensis.ResultsWe found that both habitat and host species shape the composition and diversity of the skin microbiome, with habitat having the strongest influence. Cohabitating A. jamaicensis and C. perspicillata shared more similar skin microbiomes than members of the same species (A. jamaicensis) across two habitats.DiscussionThese results suggest that in captivity, the skin microbial community is homogenised by the shared environments and individual proximities of bats living together in the same habitat, at the expense of the innate host species factors. The predominant influence of habitat suggests that environmental microorganisms or pathogens might colonize bat skin. We also propose that bat populations could differ in pathogen susceptibility depending on their immediate environment and habitat.

Highlights

Animal skin is an ecosystem inhabited by highly variable and complex communities of microorganisms (Grice & Segre, 2011), which can be divided into resident and transient flora acquired from the environment (Roth & James, 1988)
Habitat and host species both shape the composition of bat skin microbiomes
Five taxa were representative of A. jamaicensis from the Granby Zoo, whereas one and three taxa were respectively representative of A. jamaicensis and C. perspicillata from the Biodôme (Fig. 2)

Summary

Introduction

Animal skin is an ecosystem inhabited by highly variable and complex communities of microorganisms (Grice & Segre, 2011), which can be divided into resident and transient flora acquired from the environment (Roth & James, 1988). How to cite this article Lemieux-Labonté et al (2016), Environment and host species shape the skin microbiome of captive neotropical bats. A wide range of microorganisms inhabit animal skin This microbial community (microbiome) plays an important role in host defense against pathogens and disease. We aimed to determine the relative importance of habitat and host species on the bat skin microbiome. We found that both habitat and host species shape the composition and diversity of the skin microbiome, with habitat having the strongest influence. These results suggest that in captivity, the skin microbial community is homogenised by the shared environments and individual proximities of bats living together in the same habitat, at the expense of the innate host species factors. We propose that bat populations could differ in pathogen susceptibility depending on their immediate environment and habitat

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