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.
Highlights
Eukaryotic viruses have a direct impact on human health [1], while prokaryotic viruses are thought to influence human body homeostasis by affecting bacterial community structure and function [2,3,4,5]
We demonstrate the feasibility of using single-virus genomics (SVGs) to sequence the genome of uncultured DNA viruses present in human saliva, and we combine the power of viral metagenomics and SVGs to study the human salivary virome
Saliva was collected from three volunteers, and processed in parallel for viromics and SVGs (Table S1)
Summary
Eukaryotic viruses have a direct impact on human health [1], while prokaryotic viruses are thought to influence human body homeostasis by affecting bacterial community structure and function [2,3,4,5]. Culturing methods inefficiently capture naturally occurring viral genomic diversity, especially in prokaryotic viruses, and nowadays viral genomics is moving into the era of metagenomics [10,11], which overcomes some of the culture limitations. Viruses 2018, 10, 113 referred to as viromics) is the delivery of accurate and complete viral genomes from viral assemblages. Viromics struggles to assemble genomes from viral populations with
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