Next Article in Journal
Upregulation of Glucose Uptake and Hexokinase Activity of Primary Human CD4+ T Cells in Response to Infection with HIV-1
Next Article in Special Issue
“French Phage Network”—Third Meeting Report
Previous Article in Journal
Overexpression of MAP2 and NF-H Associated with Dendritic Pathology in the Spinal Cord of Mice Infected with Rabies Virus
Previous Article in Special Issue
Bacteriophage GC1, a Novel Tectivirus Infecting Gluconobacter Cerinus, an Acetic Acid Bacterium Associated with Wine-Making
Article

Deciphering the Human Virome with Single-Virus Genomics and Metagenomics

1
Department of Physiology, Genetics, and Microbiology, University of Alicante, 03690 Alicante, Spain
2
Flow Cytometry Unit: Pompeu Fabra University (UPF) and Centre for Genomic Regulation (CRG), The Barcelona Institute for Sciences and Technology (BIST), 08003 Barcelona, Spain
*
Author to whom correspondence should be addressed.
Viruses 2018, 10(3), 113; https://doi.org/10.3390/v10030113
Received: 31 January 2018 / Revised: 28 February 2018 / Accepted: 1 March 2018 / Published: 6 March 2018
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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. View Full-Text
Keywords: single-virus genomics; viral metagenomics; oral cavity; bacteriophage; virus; saliva; human; Streptococcus single-virus genomics; viral metagenomics; oral cavity; bacteriophage; virus; saliva; human; Streptococcus
Show Figures

Figure 1

MDPI and ACS Style

De la Cruz Peña, M.J.; 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, 10, 113. https://doi.org/10.3390/v10030113

AMA Style

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; 10(3):113. https://doi.org/10.3390/v10030113

Chicago/Turabian Style

De la Cruz Peña, Maria J., Francisco Martinez-Hernandez, Inmaculada Garcia-Heredia, Mónica Lluesma Gomez, Òscar Fornas, and Manuel Martinez-Garcia. 2018. "Deciphering the Human Virome with Single-Virus Genomics and Metagenomics" Viruses 10, no. 3: 113. https://doi.org/10.3390/v10030113

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop