title: Virome-associated antibiotic-resistance genes in an experimental aquaculture facility.
abstract: We report the comprehensive characterization of viral and microbial communities within an aquaculture wastewater sample, by a shotgun sequencing and 16S rRNA gene profiling metagenomic approach. Caudovirales had the largest representation within the sample, with over 50% of the total taxonomic abundance, whereas approximately 30% of the total open reading frames (ORFs) identified were from eukaryotic viruses (Mimiviridae and Phycodnaviridae). Antibiotic resistance genes (ARGs) within the virome accounted for 0.85% of the total viral ORFs and showed a similar distribution both in virome and in microbiome. Among the ARGs, those encoding proteins involved in the modulation of antibiotic efflux pumps were the most abundant. Interestingly, the taxonomy of the bacterial ORFs identified in the viral metagenome did not reflect the microbial taxonomy as deduced by 16S rRNA gene profiling and shotgun metagenomic analysis. A limited number of ARGs appeared to be mobilized from bacteria to phages or vice versa, together with other bacterial genes encoding products involved in general metabolic functions, even in the absence of any antibiotic treatment within the aquaculture plant. Thus, these results confirm the presence of a complex phage-bacterial network in the aquaculture environment.
authors.affiliation: Department of Food, Nutritional, and Environmental Sciences, University of Milan, 20133 Milan, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Colombo
authors.affiliation: Department of Food, Nutritional, and Environmental Sciences, University of Milan, 20133 Milan, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Arioli
authors.affiliation: Department of Food, Nutritional, and Environmental Sciences, University of Milan, 20133 Milan, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Guglielmetti
authors.affiliation: Fondazione Edmund Mach, Dipartimento Filiere Agroalimentari, Unità Acquacoltura e Idrobiologia, San Michele all'Adige, 38010 Trento, Italy.
authors.forename: Fernando
authors.initials: F
authors.lastname: Lunelli
authors.affiliation: Department of Food, Nutritional, and Environmental Sciences, University of Milan, 20133 Milan, Italy diego.mora@unimi.it.
authors.forename: Diego
authors.initials: D
authors.lastname: Mora
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D017756:Aquaculture; D001419:Bacteria / Q000145:classification / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics*; D001435:Bacteriophages / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004352:Drug Resistance, Microbial / Q000235:genetics; D054892:Metagenome / Q000187:drug effects; D056186:Metagenomics; D064307:Microbiota; D016366:Open Reading Frames; D062065:Wastewater / Q000382:microbiology / Q000821:virology
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D062065:Wastewater
keywords: antibiotic resistance genes; aquaculture; horizontal gene transfer; microbiome; virome