Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana

PLoS One. 2017 Nov 8;12(11):e0186943. doi: 10.1371/journal.pone.0186943. eCollection 2017.

Abstract

Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats. These sequences are related to 51 viral families known to infect a wide range of hosts (i.e., bacteria, plants, insects and vertebrates). Most viruses detected reflected the diet of bat species, with a high proportion of plant and insect-related viral families for M. molossus and a high proportion of vertebrate-related viral families for D. rotundus, highlighting its influence in shaping the viral diversity of bats. Lastly, we reconstructed the phylogenetic relationships for five vertebrate-related viral families (Nairoviridae, Circoviridae, Retroviridae, Herpesviridae, Papillomaviridae). The results showed highly supported clustering with other viral sequences of the same viral family hosted by other bat species, highlighting the potential association of viral diversity with the host's diet. These findings provide significant insight into viral bat diversity in French Guiana belonging to the Amazonian biome and emphasize that habitats and the host's dietary ecology may drive the viral diversity in the bat communities investigated.

MeSH terms

  • Animals
  • Chiroptera / genetics*
  • Chiroptera / virology
  • Ecosystem
  • French Guiana
  • Genome, Viral / genetics*
  • Insect Viruses / genetics
  • Insecta / virology
  • Metagenomics
  • Phylogeny
  • Sympatry / genetics*
  • Sympatry / physiology
  • Viruses / genetics*

Grants and funding

A. Salmier was funded by a grant from European funds (PO FSE 2007-2013) and "Investissement d’Avenir" managed by Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABEX-25-01). This study was conducted within the CAROLIA program supported by European funds (ERDF/FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie. It also received a European Commission "REGPOT-CT-2011-285837-STRonGer" grant within the FP7 and "Investissement d’Avenir" grants managed by the Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABEX-25-01). The Genomics Platform is a member of the France Génomique consortium (ANR10-INBS-09-08). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.