Freshwater metaviromics and bacteriophages: A current assessment of the state of the art in relation to Bioinformatic challenges

Evolutionary Bioinformatics

Volumn 12, Issue , 2016, Pages 25-33

  Bruder, Katherine ^a   Malki, Kema ^a   Cooper, Alexandria ^a   Sible, Emily ^a   Shapiro, Jason W ^a   Watkins, Siobhan C ^a   Putonti, Catherine ^a  

^a LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

Bacteriophages; Environmental metagenomics; Freshwater; Metaviromics

Indexed keywords

BACTERIOPHAGE; BIOGEOCHEMISTRY; BIOINFORMATICS; COMMUNITY STRUCTURE; EVOLUTION; FRESHWATER SPECIES; HORIZONTAL GENE TRANSFER; METAGENOMICS; METAVIROMICS; METHODOLOGY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUTRIENT; REVIEW; SEASONAL VARIATION; VIROLOGY; WATER SAMPLING; WEATHER;

EID: 84975292133     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S38549     Document Type: Review

References (87)

1. Cowan D, Ramond JB, Makhalanyane T, De Maayer P. Metagenomics of extreme environments. Curr Opin Microbiol. 2015;25:97-102.
2. Kembel SW, Jones E, Kline J, et al. Architectural design influences the diversity and structure of the built environment microbiome. ISME J. 2012;6(8):1469-79.
3. Yarza P, Yilmaz P, Pruesse E, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Rev Microbiol. 2014;12(9):635-45.
4. Eloe-Fadrosh EA, Paez-Espino D, Jarett J, et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 2016;7:10476.
5. Hatfull GF. Bacteriophage genomics. Curr Opin Microbiol. 2008;11(5):447-53.
6. Sharon I, Battchikova N, Aro EM, et al. Comparative metagenomics of microbial traits within oceanic viral communities. ISME J. 2011;5(7):1178-90.
7. Suttle CA. Marine viruses - major players in the global ecosystem. Nat Rev Microbiol. 2007;5(10):801-12.
8. Hendrix RW. Bacteriophage genomics. Curr Opin Microbiol. 2003;6(5):506-11.
9. Dinsdale EA, Edwards RA, Hall D, et al. Functional metagenomic profiling of nine biomes. Nature. 2008;452(7187):629-32.
10. Hurwitz BL, Sullivan MB. The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 2013;8(2):e57355.
11. Weinbauer MG, Rassoulzadegan F. Are viruses driving microbial diversification and diversity? Environ Microbiol. 2004;6(1):1-11.
12. Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature. 2009;459(7244):207-12.
13. Oh S, Caro-Quintero A, Tsementzi D, et al. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Enviorn Microbiol. 2011;77(17):6000-11.
14. Somboonna N, Assawamakin A, Wilantho A, Tangphatsornruang S, Tongsima S. Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand. BMC Genomics. 2012;13(7):S29.
15. Hugerth LW, Larsson J, Alneberg J, et al. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol. 2015;16:279.
16. Bouvier T, del Giorgio PA. Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol. 2007;9(2):287-97.
17. Ogilvie LA, Bowler LD, Caplin J, et al. Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences. Nat Commun. 2013;4:2420.
18. Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A. 2013;110(30):12450-5.
19. Koskella B, Brockhurst MA. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. 2014;38(5):916-31.
20. Abeles SR, Pride DT. Molecular bases and role of viruses in the human microbiome. J Mol Biol. 2014;426(23):3892-906.
21. Wang J, Gao Y, Zhao F. Phage-bacteria interaction network in human oral microbiome: human oral virome. Environ Microbiol. 2015. http://www.ncbi.nlm.nih.gov/pubmed/?term=26036920
22. Casjens S. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol. 2003;49(2):277-300.
23. Hatfull GF, Hendrix RW. Bacteriophages and their genomes. Curr Opin Virol. 2011;1:298-303.
24. Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol. 2012;10(9):607-17.
25. Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods. 2013;95(3):401-14.
26. Schirmer M, D’Amore R, Ijaz UZ, Hall N, Quince C. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics. 2016;17(1):125.
27. Yang X, Liu D, Liu F, et al. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics. 2013;14:33.
28. Sato Y, Kojima K, Nariai N, et al. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing. BMC Genomics. 2014;15:664.
29. Crusoe MR, Alameldin HF, Awad S, et al. The khmer software package: enabling efficient nucleotide sequence analysis. F1000Res. 2015;4:900.
30. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9.
31. Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-77.
32. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010;11(5):473-83.
33. Nagarajan N, Pop M. Sequence assembly demystified. Nat Rev Genet. 2013; 14(3):157-67.
34. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10.
35. Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002;12(4): 656-64. [Article published online before March 2002].
36. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2016;44(D1):D67-72.
37. O’Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733-45.
38. Overbeek R, Begley T, Butler RM, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33(17):5691-702.
39. Wilke A, Bischof J, Gerlach W, et al. The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Res. 2016;44(D1):D590-4.
40. Huson DH, Weber N. Microbial community analysis using MEGAN. Methods Enzymol. 2013;531:465-85.
41. Roux S, Tournayre J, Mahul A, Debroas D, Enault F. Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics. 2014;15:76.
42. Wommack KE, Bhavsar J, Polson SW, et al. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci. 2012;6(3):427-39.
43. Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) Program; KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course; University of California - Los Angeles Research Immersion Laboratory in Virology; Phage Hunters Integrating Research and Education (PHIRE) Program. Complete genome sequences of 63 mycobacteriophages. Genome Announc. 2013;1(6):e847-913.
44. Angly FE, Felts B, Breitbart M, et al. The marine viromes of four oceanic regions. PLoS Biol. 2006;4(11):e368.
45. López-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, Alcami A. High diversity of the viral community from an Antarctic Lake. Science. 2009;326(5954):858-61.
46. Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. Metagenomic analysis of viruses in reclaimed water. Environ Microbiol. 2009;11(11):2806-20.
47. Leplae R. ACLAME: a classification of mobile genetic elements. Nucleic Acids Res. 2004;32(90001):45D-9D.
48. Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
49. Hatzopoulos T, Watkins S, Putonti C. PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets. Microbial Genomics. 2016. [In Press].
50. Rosario K, Breitbart M. Exploring the viral world through metagenomics. Curr Opin Virol. 2011;1(4):289-97.
51. Mohiuddin M, Schellhorn HE. Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis. Front Microbiol. 2015;6:960.
52. Steward GF, Culley AI, Mueller JA, Wood-Charlson EM, Belcaid M, Poisson G. Are we missing half of the viruses in the ocean? ISME J. 2013;7(3):672-9.
53. López-Bueno A, Rastrojo A, Peiró R, Arenas M, Alcamí A. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Mol Ecol. 2015;24(19):4812-25.
54. Green J, Rahman F, Saxton M, Williamson K. Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA. Aquat Microb Ecol. 2015;75(2):117-28.
55. Bergh O, Børsheim KY, Bratbak G, Heldal M. High abundance of viruses found in aquatic environments. Nature. 1989;340(6233):467-8.
56. Breitbart M, Salamon P, Andresen B, et al. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A. 2002;99(22):14250-5.
57. Fancello L, Trape S, Robert C, et al. Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. ISME J. 2013;7(2):359-69.
58. Tseng CH, Chiang PW, Shiah FK, et al. Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances. ISME J. 2013;7(12):2374-86.
59. Skvortsov T, de Leeuwe C, Quinn JP, et al. Metagenomic characterisation of the viral community of Lough Neagh, the largest freshwater lake in Ireland. PLoS One. 2016;11(2):e0150361.
60. Roux S, Enault F, Robin A, et al. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One. 2012;7(3):e33641.
61. Jones AC, Liao TSV, Najar FZ, Roe BA, Hambright KD, Caron DA. Seasonality and disturbance: annual pattern and response of the bacterial and microbial eukaryotic assemblages in a freshwater ecosystem. Environ Microbiol. 2013;15(9):2557-72.
62. Ortmann AC, Ortell N. Changes in free-living bacterial community diversity reflect the magnitude of environmental variability. FEMS Microbiol Ecol. 2014;87(1):291-301.
63. Dutilh BE, Schmieder R, Nulton J, et al. Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics. 2012;28(24): 3225-31.
64. Aguirre de Cárcer D, Lopez-Bueno A, Pearce DA, Alcami A. Biodiversity and distribution of polar freshwater DNA viruses. Sci Adv. 2015;1(5):e1400127.
65. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brüssow H. Phage as agents of lateral gene transfer. Curr Opin Microbiol. 2003;6(4):417-24.
66. Watkins SC, Kuehnle N, Ruggeri CA, et al. Assessment of a metaviromic dataset generated from nearshore Lake Michigan. Marine Fresh Res. 2015. [In Press].
67. Dutilh BE, Cassman N, McNair K, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498.
68. Dutilh BE, Huynen MA, Strous M. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics. 2009;25(21):2878-81.
69. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):R46.
70. Malki K, Bruder K, Putonti C. Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches. Data Brief. 2015;5:556-9.
71. Malki K, Kula A, Bruder K, et al. Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla. Virol J. 2015;12:164.
72. Ceyssens P, Miroshnikov K, Mattheus W, et al. Comparative analysis of the widespread and conserved PB1-like viruses infecting Pseudomonas aeruginosa. Enviorn Microbiol. 2009;11(11):2874-83.
73. Székely AJ, Breitbart M. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. FEMS Microbiol Lett. 363(6). pii: fnw027. http://www.ncbi.nlm.nih.gov/pubmed/?term=26850442
74. Djikeng A, Kuzmickas R, Anderson NG, Spiro DJ. Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One. 2009;4(9):e7264.
75. Adriaenssens EM, van Zyl LJ, Cowan DA, Trindade MI. Metaviromics of Namib Desert salt pans: a novel lineage of haloarchaeal salterproviruses and a rich source of ssDNA viruses. Viruses. 2016;8(1):14.
76. Zhang T, Breitbart M, Lee WH, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2006;4(1):e3.
77. Krishnamurthy SR, Janowski AB, Zhao G, Barouch D, Wang D. Hyperexpansion of RNA bacteriophage diversity. PLoS Biol. 2016;14(3):e1002409.
78. Williamson KE, Radosevich M, Smith DW, Wommack KE. Incidence of lysogeny within temperate and extreme soil environments. Environ Microbiol. 2007;9(10):2563-74.
79. Fierer N, Breitbart M, Nulton J, et al. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Enviorn Microbiol. 2007;73(21):7059-66.
80. Zablocki O, van Zyl L, Adriaenssens EM, et al. High diversity of tailed phages, eukaryotic viruses and virophage-like elements in the metaviromes of Antartic soils. Appl Environ Microbiol. 2014;80(22):6888-97.
81. Parsley LC, Consuegra EJ, Thomas SJ, et al. Census of the viral metagenome within an activated sludge microbial assemblage. Appl Environ Microbiol. 2010; 76(8):2673-7.
82. Yooseph S, Sutton G, Rusch DB, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007; 5(3):e16.
83. Brum JR, Ignacio-Espinoza JC, Roux S, et al. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science. 2015;348(6237):1261498.
84. Brum JR, Hurwitz BL, Schofield O, Ducklow HW, Sullivan MB. Seasonal time bombs: dominant temperate viruses affect southern ocean microbial dynamics. ISME J. 2016;10(2):437-49.
85. Clokie MRJ, Kropinski A, eds. Bacteriophages. Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions. New York City, NY: Human Press; 2009.
86. Santiago-Rodriguez TM, Naidu M, Abeles SR, Boehm TK, Ly M, Pride DT. Transcriptome analysis of bacteriophage communities in periodontal health and disease. BMC Genomics. 2015;16:549.
87. Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev. 2016;40(2):258-72.