1. Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana
- Author
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LACOSTE, Vincent, SALMIER, Arielle, TIRERA, Sourakhata, FRANC, Alain, DARCISSAC, Edith, DONATO, Damien, BOUCHIER, Christiane, LAVERGNE, Anne, DE THOISY, Benoit, FORRESTER, Naomi, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris], 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)., We acknowledge François Catzeflis and Marguerite Delaval for useful discussions on the biology, ecology and dynamics of bats. All field volunteers and owners and/or managers of capture sites are warmly acknowledged for their assistance in captures. We thank the INDA and C3BI teams at the Institut Pasteur and UMR BIOGECO for their technical support and access to the clusters. We thank L. Ma and M. Tichit for technical assistance., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Génomique (Plate-Forme), ANR-10-LABX-25-01/10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, and Institut Pasteur [Paris] (IP)
- Subjects
Topography ,Molossus molossus ,Forests ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Pathology and Laboratory Medicine ,amazonie ,Chiroptera ,Bats ,MESH: Animals ,MESH: Ecosystem ,lcsh:Science ,MESH: Phylogeny ,Phylogeny ,Mammals ,Fruit Bats ,Eukaryota ,Phylogenetic Analysis ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Terrestrial Environments ,French Guiana ,Sympatric speciation ,Medical Microbiology ,Viral Pathogens ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,MESH: Viruses/genetics ,MESH: Metagenomics ,Bioinformatics ,030106 microbiology ,Zoology ,Sequence Databases ,hématophage ,Microbiology ,03 medical and health sciences ,Phylogenetics ,MESH: Sympatry/genetics ,forêt primaire ,espèce réservoir ,Evolutionary Systematics ,Saliva ,Microbial Pathogens ,Ecosystem ,Host (biology) ,lcsh:R ,Ecology and Environmental Sciences ,Organisms ,Biology and Life Sciences ,15. Life on land ,030104 developmental biology ,desmodus rotundus ,lcsh:Q ,Metagenomics ,0301 basic medicine ,MESH: Genome, Viral/genetics ,Insecta ,Range (biology) ,Physiology ,viruses ,MESH: Insecta/virology ,lcsh:Medicine ,Database and Informatics Methods ,Medicine and Health Sciences ,MESH: Chiroptera/virology ,Data Management ,Multidisciplinary ,Ecology ,MESH: Insect Viruses/genetics ,Body Fluids ,Sympatry ,Caves ,Viruses ,Vertebrates ,Anatomy ,Pathogens ,épidémie ,Sequence Analysis ,Research Article ,Computer and Information Sciences ,Herpesviruses ,Insect Viruses ,Genome, Viral ,Biology ,Research and Analysis Methods ,Ecosystems ,néotropique ,chauve souris ,MESH: Chiroptera/genetics ,MESH: French Guiana ,Animals ,Human virome ,population virale ,Taxonomy ,[SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health ,Evolutionary Biology ,Landforms ,insectivore ,Insectivore ,Geomorphology ,biology.organism_classification ,MESH: Sympatry/physiology ,Biological Databases ,Amniotes ,Desmodus rotundus ,Earth Sciences ,DNA viruses - Abstract
International audience; Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensifica-tion, 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, Herpesviri-dae, 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.
- Published
- 2017