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


METHODS
We 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.


RESULTS
We 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.


CONCLUSIONS
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. 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.
Département de Sciences Biologiques, Université de Montréal , Montréal , Canada.
Virginie
V
Lemieux-Labonté
Département de Sciences Biologiques, Université de Montréal , Montréal , Canada.
Nicolas
N
Tromas
Département de Sciences Biologiques, Université de Montréal , Montréal , Canada.
B Jesse
BJ
Shapiro
Département de Sciences Biologiques, Université de Montréal , Montréal , Canada.
François-Joseph
FJ
Lapointe
Bat skin microbiome; Habitat–microbiome interaction; Host–microbiome interaction
Genome Biol. 2011 Jun 24;12(6):R60
21702898
Elife. 2013 Apr 16;2:e00458
23599893
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
16820507
Appl Environ Microbiol. 2013 Nov;79(21):6593-603
23974136
ISME J. 2013 Jun;7(6):1092-101
23407313
Genome Res. 2013 Oct;23(10):1715-20
23804402
PLoS One. 2010 Mar 10;5(3):e9490
20224823
ISME J. 2012 Mar;6(3):588-96
21955991
ISME J. 2011 Feb;5(2):169-72
20827291
Annu Rev Microbiol. 1988;42:441-64
3144238
Nature. 2011 Oct 26;480(7377):376-8
22031324
Fungal Biol. 2013 Sep;117(9):638-49
24012303
ISME J. 2014 Apr;8(4):830-40
24335825
Mol Ecol. 2012 Jun;21(11):2617-27
22519571
PLoS Biol. 2010 Nov 16;8(11):e1000546
21103409
Front Microbiol. 2015 May 19;6:447
26042099
Methods Enzymol. 2013;531:353-70
24060130
BMC Microbiol. 2014 Sep 26;14:246
25253442
Microbiome. 2015 Dec 21;3:76
26689946
J Dermatol Sci. 2009 Sep;55(3):144-9
19574028
PLoS One. 2015 Oct 28;10(10):e0141842
26510185
Biometrics. 2006 Mar;62(1):245-53
16542252
Nat Methods. 2010 May;7(5):335-6
20383131
PLoS One. 2013 Apr 22;8(4):e61217
23630581
PLoS One. 2015 Jul 13;10(7):e0132860
26168244
Mol Ecol. 2014 Mar;23(6):1238-50
24171949
ISME J. 2011 Oct;5(10):1595-608
21472014
Genome Med. 2012 Oct 10;4(10):77
23050952
ISME J. 2014 Nov;8(11):2207-17
24858782
PLoS Comput Biol. 2014 Apr 03;10(4):e1003531
24699258
Appl Environ Microbiol. 2005 Dec;71(12):8228-35
16332807
PLoS One. 2015 Apr 08;10(4):e0121329
25853558
PeerJ. 2013 Sep 12;1:e157
24058885
Bioinformatics. 2010 Oct 1;26(19):2460-1
20709691
Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17994-9
19004758
Nat Rev Microbiol. 2011 Apr;9(4):244-53
21407241
PLoS One. 2014 Jan 08;9(1):e83197
24421875
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22
20534432
J Chem Ecol. 2008 Nov;34(11):1422-9
18949519
Appl Environ Microbiol. 2007 Mar;73(5):1576-85
17220268