Deciphering the human virome with single-virus genomics and metagenomics

Viruses

Volumn 10, Issue 3, 2018, Pages

  De La Cruz Peña, Maria José ^a   Martinez Hernandez, Francisco ^a   Garcia Heredia, Inmaculada ^a   Gomez, Mónica Lluesma ^a   Fornas, Òscar ^b   Martinez Garcia, Manuel ^a  

^a UNIVERSITY OF ALICANTE   (Spain)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

Bacteriophage; Human; Oral cavity; Saliva; Single virus genomics; Streptococcus; Viral metagenomics; Virus

Indexed keywords

ACTINOMYCES; ARTICLE; BACTERIOPHAGE; CLINICAL ARTICLE; COMMUNITY STRUCTURE; FLUORESCENCE; GENE AMPLIFICATION; GENUS; HUMAN; METAGENOMICS; MOUTH CAVITY; NONHUMAN; SALIVA; STREPTOCOCCUS; VIRUS GENE; BIOLOGY; HIGH THROUGHPUT SEQUENCING; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; MOUTH; PROCEDURES; VIROLOGY; VIRUS GENOME;

COMPUTATIONAL BIOLOGY; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; MOUTH; SALIVA;

EID: 85043330406     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v10030113     Document Type: Article

References (41)

1. Bouziat, R.; Hinterleitner, R.; Brown, J.J.; Stencel-Baerenwald, J.E.; Ikizler, M.; Mayassi, T.; Meisel, M.; Kim, S.M.; Discepolo, V.; Pruijssers, A.J.; et al. Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Science 2017, 356, 44–50. [CrossRef] [PubMed]
2. Barr, J.J.; Auro, R.; Furlan, M.; Whiteson, K.L.; Erb, M.L.; Pogliano, J.; Stotland, A.; Wolkowicz, R.; Cutting, A.S.; Doran, K.S., et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl. Acad. Sci. USA 2013, 110, 10771–10776. [CrossRef] [PubMed]
3. Minot, S.; Sinha, R.; Chen, J.; Li, H.; Keilbaugh, S.A.; Wu, G.D.; Lewis, J.D.; Bushman, F.D. The human gut virome: Inter-individual variation and dynamic response to diet. Genome Res. 2011, 21, 1616–1625. [CrossRef] [PubMed]
4. Haynes, M.; Rohwer, F. The Human Virome. In Metagenomics of the Human Body; Springer: New York, NY, USA, 2011; pp. 63–77.
5. Willner, D.; Furlan, M.; Haynes, M.; Schmieder, R.; Angly, F.E.; Silva, J.; Tammadoni, S.; Nosrat, B.; Conrad, D.; Rohwer, F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE 2009, 4, e7370. [CrossRef] [PubMed]
6. Wylie, K.M.; Weinstock, G.M.; Storch, G.A. Emerging view of the human virome. Transl. Res. 2012, 160, 283–290. [CrossRef] [PubMed]
7. Lecuit, M.; Eloit, M. The human virome: New tools and concepts. Trends Microbiol. 2013, 21, 510–515. [CrossRef] [PubMed]
8. Williams, S.C.P. The other microbiome. Proc. Natl. Acad. Sci. USA 2013, 110, 2682–2684. [CrossRef] [PubMed]
9. Wylie, K.M.; Mihindukulasuriya, K.A.; Zhou, Y.; Sodergren, E.; Storch, G.A.; Weinstock, G.M. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol. 2014, 12, 71. [CrossRef] [PubMed]
10. Simmonds, P.; Adams, M.J.; Benkő, M.; Breitbart, M.; Brister, J.R.; Carstens, E.B.; Davison, A.J.; Delwart, E.; Gorbalenya, A.E.; Harrach, B.; et al. Consensus statement: Virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 2017, 15, 161–168. [CrossRef] [PubMed]
11. Duraisamy, R. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu. Rev. Microbiol. 2016. [CrossRef]
12. Martinez-Hernandez, F.; Fornas, O.; Lluesma Gomez, M.; Bolduc, B.; de La Cruz Peña, M.J.; Martínez, J.M.; Anton, J.; Gasol, J.M.; Rosselli, R.; Rodriguez-Valera, F.; et al. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat. Commun. 2017, 8, 15892. [CrossRef] [PubMed]
13. Roux, S.; Emerson, J.B.; Eloe-Fadrosh, E.A.; Sullivan, M.B. Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ 2017, 5, e3817. [CrossRef] [PubMed]
14. Allen, L.Z.; Ishoey, T.; Novotny, M.A.; McLean, J.S.; Lasken, R.S.; Williamson, S.J. Single virus genomics: A new tool for virus discovery. PLoS ONE 2011, 6, e17722. [CrossRef] [PubMed]
15. Stepanauskas, R.; Fergusson, E.A.; Brown, J.; Poulton, N.J.; Tupper, B.; Labonté, J.M.; Becraft, E.D.; Brown, J.M.; Pachiadaki, M.G.; Povilaitis, T.; et al. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat. Commun. 2017, 8, 1–10.
16. Wilson, W.H.; Gilg, I.C.; Moniruzzaman, M.; Field, E.K.; Koren, S.; LeCleir, G.R.; Martínez Martínez, J.; Poulton, N.J.; Swan, B.K.; Stepanauskas, R.; et al. Genomic exploration of individual giant ocean viruses. ISME J. 2017, 11, 1736–1745. [CrossRef] [PubMed]
17. Lasken, R.S.; McLean, J.S. Recent advances in genomic DNA sequencing of microbial species from single cells. Nat. Rev. Genet. 2014, 15, 577–584. [CrossRef] [PubMed]
18. Pride, D.T.; Salzman, J.; Haynes, M.; Rohwer, F.; Davis-Long, C.; White, R.A.; Loomer, P.; Armitage, G.C.; Relman, D.A. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 2012, 6, 915–926. [CrossRef] [PubMed]
19. Brussaard, C.P.D. Optimization of Procedures for Counting Viruses by Flow Cytometry. Appl. Environ. Microbiol. 2004, 70, 1506–1513. [CrossRef] [PubMed]
20. Schmieder, R.; Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27, 863–864. [CrossRef] [PubMed]
21. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19, 455–477. [CrossRef] [PubMed]
22. Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28, 1647–1649. [CrossRef] [PubMed]
23. Laurence, M.; Hatzis, C.; Brash, D.E. Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS ONE 2014, 9, e97876. [CrossRef] [PubMed]
24. Tennessen, K.; Andersen, E.; Clingenpeel, S.; Rinke, C.; Lundberg, D.S.; Han, J.; Dangl, J.L.; Ivanova, N.; Woyke, T.; Kyrpides, N.; et al. ProDeGe: A computational protocol for fully automated decontamination of genomes. ISME J. 2015, 10, 269–272. [CrossRef] [PubMed]
25. Roux, S.; Tournayre, J.; Mahul, A.; Debroas, D.; Enault, F. Metavir 2: New tools for viral metagenome comparison and assembled virome analysis. BMC Bioinf. 2014, 15, 76. [CrossRef] [PubMed]
26. Markowitz, V.M.; Chen, I.-M.A.; Chu, K.; Szeto, E.; Palaniappan, K.; Pillay, M.; Ratner, A.; Huang, J.; Pagani, I.; Tringe, S.; et al. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 2014, 42, D568–D573. [CrossRef] [PubMed]
27. Camacho, C.; Coulouris, G.; Avagyan, V.; Ma, N.; Papadopoulos, J.; Bealer, K.; Madden, T.L. BLAST+: Architecture and applications. BMC Bioinf. 2009, 10, 421. [CrossRef] [PubMed]
28. Eddy, S.R. Profile hidden Markov models. Bioinformatics 1998, 14, 755–763. [CrossRef] [PubMed]
29. Rutherford, K.; Parkhill, J.; Crook, J.; Horsnell, T.; Rice, P.; Rajandream, M.-A.; Barrell, B. Artemis: Sequence visualization and annotation. Bioinformatics 2000, 16, 944–945. [CrossRef] [PubMed]
30. Rice, P.; Longden, I.; Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000, 16, 276–277. [CrossRef]
31. Lê, S.; Josse, J.; Husson, F. FactoMineR: An R Package for Multivariate Analysis. J. Stat. Softw. 2008, 25, 1–18. [CrossRef]
32. Rodriguez-R L.M.; Konstantinidis, K.T. The enveomics collection: A toolbox for specialized analyses of microbial genomes and metagenomes. Peer J 2016. [CrossRef]
33. Roux, S.; Brum, J.R.; Dutilh, B.E.; Sunagawa, S.; Duhaime, M.B.; Loy, A.; Poulos, B.T.; Solonenko, N.; Lara, E.; Poulain, J.; et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 2016, 537, 689–693. [CrossRef] [PubMed]
34. Noguchi, H.; Taniguchi, T.; Itoh, T. MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 2008, 15, 387–396. [CrossRef] [PubMed]
35. Enright, A.J.; van Dongen, S.; Ouzounis, C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30, 1575–1584. [CrossRef] [PubMed]
36. Bolduc, B.; Jang, H.; Doulcier, G.; You, Z.-Q.; Roux, S.; Sullivan, M.B. vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ 2017, 5, e3243. [CrossRef] [PubMed]
37. Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498–2504. [CrossRef] [PubMed]
38. Abeles, S.R.; Robles-Sikisaka, R.; Ly, M.; Lum, A.G.; Salzman, J.; Boehm, T.K.; Pride, D.T. Human oral viruses are personal, persistent and gender-consistent. ISME J. 2014, 8, 1753–1767. [CrossRef] [PubMed]
39. Gawad, C.; Koh, W.; Quake, S.R. Single-cell genome sequencing: Current state of the science. Nat. Rev. Genet. 2016, 17, 175–188. [CrossRef] [PubMed]
40. Forterre, P.; Soler, N.; Krupovic, M.; Marguet, E.; Ackermann, H.-W. Fake virus particles generated by fluorescence microscopy. Trends Microbiol. 2013, 21, 1–5. [CrossRef] [PubMed]
41. Biller, S.J.; Schubotz, F.; Roggensack, S.E.; Thompson, A.W.; Summons, R.E.; Chisholm, S.W. Bacterial vesicles in marine ecosystems. Science 2014, 343, 183–186. [CrossRef] [PubMed]