viruses Article Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity 1, 2, 1, 1 2 Ivana Šimi´c y, Tomaž Mark Zorec y , Ivana Lojki´c * , Nina Kreši´c , Mario Poljak , Florence Cliquet 3 , Evelyne Picard-Meyer 3, Marine Wasniewski 3 , Vida Zrnˇci´c 4, Andela¯ Cukuši´c´ 4 and Tomislav Bedekovi´c 1 1 Laboratory for Rabies and General Virology, Department of Virology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
[email protected] (I.Š.);
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[email protected] (T.B.) 2 Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, 1000 Ljubljana, Slovenia;
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[email protected] (M.P.) 3 Nancy Laboratory for Rabies and Wildlife, ANSES, 51220 Malzéville, France; fl
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[email protected] (M.W.) 4 Croatian Biospeleological Society, 10000 Zagreb, Croatia;
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[email protected] (A.C.)´ * Correspondence:
[email protected] These authors contributed equally to this work. y Received: 21 July 2020; Accepted: 11 August 2020; Published: 14 August 2020 Abstract: To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing.