Deciphering the Human Virome with Single-Virus Genomics and Metagenomics

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• dc.contributor.author de la Cruz Peña, María Joseca
• dc.contributor.author Martínez Hernández, Franciscoca
• dc.contributor.author García Heredia, Inmaculadaca
• dc.contributor.author Lluesma Gómez, Mónicaca
• dc.contributor.author Fornas Carreño, Oscarca
• dc.contributor.author Martínez García, Manuelca
• dc.date.accessioned 2018-03-23T11:54:26Z
• dc.date.available 2018-03-23T11:54:26Z
• dc.date.issued 2018
• dc.description.abstract Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities. Here, we applied single-virus genomics (SVGs) to natural human salivary samples in combination with viral metagenomics to gain some insights into the viral community structure of the oral cavity. Saliva samples were processed for viral metagenomics (n = 15) and SVGs (n = 3). A total of 1328 uncultured single viruses were sorted by fluorescence-activated virus sorting followed by whole genome amplification. Sequencing of 24 viral single amplified genomes (vSAGs) showed that half of the vSAGs contained viral hallmark genes. Among those bona fide viruses, the uncultured single virus 92-C13 putatively infecting oral Streptococcus-like species was within the top ≈10 most abundant viruses in the oral virome. Viral gene network and viral metagenomics analyses of 439 oral viruses from cultures, metagenomics, and SVGs revealed that salivary viruses were tentatively structured into ≈200 major viral clusters, corresponding to approximately genus-level groupings. Data showed that none of the publicly available viral isolates, excepting an Actinomyces phage, were significantly abundant in the oral viromes. In addition, none of the obtained viral contigs and vSAGs from this study were present in all viromes. Overall, the data demonstrates that most viral isolates are not naturally abundant in saliva, and furthermore, the predominant viruses in the oral cavity are yet uncharacterized. Results suggest a variable, complex, and interpersonal viral profile. Finally, we demonstrated the power of SVGs in combination with viral metagenomics to unveil the genetic information of the uncultured viruses of the human virome.
• dc.description.sponsorship This work has been supported by the Spanish Ministry of Economy and Competitiveness (refs. CGL2013-40564-R and SAF2013-49267-EXP), the Generalitat Valenciana (refs. ACOM/2015/133 and ACIF/2015/332), and the Gordon and Betty Moore Foundation (grant 5334). We thank the English editor Karen Neller.
• dc.format.mimetype application/pdf
• dc.identifier.citation de la Cruz Peña MJ, Martinez-Hernandez F, Garcia-Heredia I, Lluesma Gomez M, Fornas Ò, Martinez-Garcia M. Deciphering the Human Virome with Single-Virus Genomics and Metagenomics. Viruses. 2018 Mar 6;10(3):113. DOI: 10.3390/v10030113
• dc.identifier.doi http://dx.doi.org/10.3390/v10030113
• dc.identifier.issn 1999-4915
• dc.identifier.uri http://hdl.handle.net/10230/34255
• dc.language.iso eng
• dc.publisher MDPIca
• dc.relation.ispartof Viruses. 2018 Mar 6;10(3):113
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/CGL2013-40564-R
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2013-49267-EXP
• dc.rights © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open accessarticle distributed under the terms and conditions of the Creative Commons Attribution(CC BY) license (http://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Single-virus genomics
• dc.subject.keyword Viral metagenomics
• dc.subject.keyword Oral cavity
• dc.subject.keyword Bacteriophage
• dc.subject.keyword Streptococcus
• dc.title Deciphering the Human Virome with Single-Virus Genomics and Metagenomicsca
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion