Skip to main content

Bacteriophage Discovery and Genomics

  • 562 Accesses

Abstract

Bacteriophages have offered opportunities for promoting student education for many years. The advancement of high throughput DNA sequencing technologies, however, has now paved the way for fuller student engagement in phage discovery and genomics. Because of the extraordinarily high diversity of phage genomes, there is a near-limitless resource of bacteriophages that can be isolated from the environment using a bacterial host of one’s choice, with strong prospects of isolating a phage that is replete with genetic novelty. The phage discovery and genomics platform is imbued with flexibility and has been implemented as open-ended research experiences for high school and undergraduate students in the Phage Hunters Integrating Research and Education (PHIRE) program, as an intense 2-week workshop in the Mycobacterial Genetic Course in Durban South Africa, and as a community of institutions providing course-based research experiences for freshman undergraduates in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. Here, I discuss the essential components of the phage discovery and genomic platform, three different configurations in which it has been implemented, and review the insights into phage diversity and genomics that have been gleaned.

Keywords

  • Phage Discovery
  • Genomics Platform
  • Mycobacterial Genetics
  • Phage Isolation
  • Smegmatis

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

References

  • Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F (2006) The marine viromes of four oceanic regions. PLoS Biol 4(11):e368

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Auchincloss LC, Laursen SL, Branchaw JL, Eagan K, Graham M, Hanauer DI, Lawrie G, McLinn CM, Pelaez N, Rowland S, Towns M, Trautmann NM, Varma-Nelson P, Weston TJ, Dolan EL (2014) Assessment of course-based undergraduate research experiences: a meeting report. CBE Life Sci Educ 13(1):29–40

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Bergh O, Borsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340(6233):467–468

    CAS  CrossRef  PubMed  Google Scholar 

  • Bernal CL, Berkowitz VE, Cahill JL, Rasche ES, Kuty Everett GF (2015) Complete genome sequence of Citrobacter freundii myophage Michonne. Genome Announc 3(5). doi:10.1128/genomeA.01134–15. PubMed PMID: 26430047; PubMed Central PMCID: PMCPMC4591319

    Google Scholar 

  • Brizendine AM, Rousseau S, Hernandez AC, Kuty Everett GF (2015) Complete genome sequence of Bacillus megaterium siphophage Stahl. Genome Announc 3(4). doi:10.1128/genomeA.00857–15. PubMed PMID: 26251491; PubMed Central PMCID: PMCPMC4541283

    Google Scholar 

  • Brum JR, Sullivan MB (2015) Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol 13(3):147–159

    CAS  CrossRef  PubMed  Google Scholar 

  • Chan BK, Abedon ST, Loc-Carrillo C (2013) Phage cocktails and the future of phage therapy. Future Microbiol 8(6):769–783

    CAS  CrossRef  PubMed  Google Scholar 

  • Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF (2011) Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12:395

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Danovaro R, Corinaldesi C, Dell’anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA (2011) Marine viruses and global climate change. FEMS Microbiol Rev 35(6):993–1034

    CAS  CrossRef  PubMed  Google Scholar 

  • Doan DP, Lessor LE, Hernandez AC, Kuty Everett GF (2015) Complete genome sequence of enterotoxigenic Escherichia coli siphophage Seurat. Genome Announc 3(1). doi:10.1128/genomeA.00044–15. PubMed PMID: 25720682; PubMed Central PMCID: PMCPMC4342423

    Google Scholar 

  • Eagan MK Jr, Sharkness J, Hurtado S, Mosqueda CM, Chang MJ (2011) Engaging undergraduates in science research: not just about faculty willingness. Res High Educ 52(2):151–177

    CrossRef  PubMed  Google Scholar 

  • Eagan MK, Hurtado S, Chang MJ, Garcia GA, Herrera FA, Garibay JC (2013) Making a difference in science education: the impact of undergraduate research programs. Am Educ Res J 50(4):683–713

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Edwards GB, Luna AJ, Hernandez AC, Kuty Everett GF (2015) Complete genome sequence of Citrobacter freundii myophage Moon. Genome Announc 3(1). doi:10.1128/genomeA.01427–14. PubMed PMID: 25635027; PubMed Central PMCID: PMCPMC4319498

    Google Scholar 

  • Farmer NG, Wood TL, Chamakura KR, Kuty Everett GF (2013) Complete genome of Acinetobacter baumannii N4-Like Podophage Presley. Genome Announc 1(6). doi:10.1128/genomeA.00852–13. PubMed PMID: 24309722; PubMed Central PMCID: PMCPMC3853045

    Google Scholar 

  • Ford ME, Sarkis GJ, Belanger AE, Hendrix RW, Hatfull GF (1998a) Genome structure of mycobacteriophage D29: implications for phage evolution. J Mol Biol 279(1):143–164

    CAS  CrossRef  PubMed  Google Scholar 

  • Ford ME, Stenstrom C, Hendrix RW, Hatfull GF (1998b) Mycobacteriophage TM4: genome structure and gene expression. Tuber Lung Dis 79(2):63–73

    CAS  CrossRef  PubMed  Google Scholar 

  • Hambly E, Suttle CA (2005) The viriosphere, diversity, and genetic exchange within phage communities. Curr Opin Microbiol 8(4):444–450

    CAS  CrossRef  PubMed  Google Scholar 

  • Hanauer DI, Jacobs-Sera D, Pedulla ML, Cresawn SG, Hendrix RW, Hatfull GF (2006) Inquiry learning. Teaching scientific inquiry. Science 314(5807):1880–1881

    CAS  CrossRef  PubMed  Google Scholar 

  • Hanauer D, Hatfull GF, Jacobs-Sera D (2009) Active assessment: assessing scientific inquiry. Springer, New York

    CrossRef  Google Scholar 

  • Hatfull GF (2010) Bacteriophage research: gateway to learning science. Microbe 5:243–250

    Google Scholar 

  • Hatfull GF (2015a) Dark matter of the biosphere: the amazing world of bacteriophage diversity. J Virol 89(16):8107–8110

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  • Hatfull GF (2015b) Innovations in undergraduate science education: going viral. J Virol 89(16):8111–8113

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  • Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR Jr, Lawrence JG, Hendrix RW (2006) Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet 2(6):e92

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyte NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O’Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW (2010) Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J Mol Biol 397(1):119–143

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  • Hendrix RW (1999) The long evolutionary reach of viruses. Curr Biol 9(24):914–917

    CrossRef  Google Scholar 

  • Hendrix RW (2002) Bacteriophages: evolution of the majority. Theor Popul Biol 61(4):471–480

    CrossRef  PubMed  Google Scholar 

  • Hunter A-B, Laursen SL, Seymour E (2007) Becoming a scientist: the role of undergraduate research in students’ cognitive, personal, and professional development. Sci Educ 91(1):36–74

    CrossRef  Google Scholar 

  • Jacobs WR Jr, Tuckman M, Bloom BR (1987) Introduction of foreign DNA into mycobacteria using a shuttle phasmid. Nature 327(6122):532–535

    CAS  CrossRef  PubMed  Google Scholar 

  • Jacobs-Sera D, Marinelli LJ, Bowman C, Broussard GW, Guerrero Bustamante C, Boyle MM, Petrova ZO, Dedrick RM, Pope WH, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Sea-Phages Program, Modlin RL, Hendrix RW, Hatfull GF (2012) On the nature of mycobacteriophage diversity and host preference. Virology 434(2):187–201

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  • Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ, Denver DR, Dunbar D, Elgin SC, Findley AM, Gissendanner CR, Golebiewska UP, Guild N, Hartzog GA, Grillo WH, Hollowell GP, Hughes LE, Johnson A, King RA, Lewis LO, Li W, Rosenzweig F, Rubin MR, Saha MS, Sandoz J, Shaffer CD, Taylor B, Temple L, Vazquez E, Ware VC, Barker LP, Bradley KW, Jacobs-Sera D, Pope WH, Russell DA, Cresawn SG, Lopatto D, Bailey CP, Hatfull GF (2014) A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. MBio 5(1):e01051–e01013

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Lerma RA, Tidwell TJ, Cahill JL, Rasche ES, Kuty Everett GF (2015) Complete genome sequence of Caulobacter crescentus podophage Percy. Genome Announc 3(6). doi:10.1128/genomeA.01373–15. PubMed PMID: 26607888; PubMed Central PMCID: PMCPMC4661307

    Google Scholar 

  • Lopatto D (2007) Undergraduate research experiences support science career decisions and active learning. CBE Life Sci Educ 6(4):297–306

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Mediavilla J, Jain S, Kriakov J, Ford ME, Duda RL, Jacobs WR Jr, Hendrix RW, Hatfull GF (2000) Genome organization and characterization of mycobacteriophage Bxb1. Mol Microbiol 38(5):955–970

    CAS  CrossRef  PubMed  Google Scholar 

  • Mijalis EM, Lessor LE, Cahill JL, Rasche ES, Kuty Everett GF (2015) Complete genome sequence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae myophage Miro. Genome Announc 3(5). doi:10.1128/genomeA.01137–15. PubMed PMID: 26430050; PubMed Central PMCID: PMCPMC4591322

    Google Scholar 

  • Mokili JL, Rohwer F, Dutilh BE (2012) Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2(1):63–77

    CAS  CrossRef  PubMed  Google Scholar 

  • Nobrega FL, Costa AR, Kluskens LD, Azeredo J (2015) Revisiting phage therapy: new applications for old resources. Trends Microbiol 23(4):185–191

    CAS  CrossRef  PubMed  Google Scholar 

  • Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, Brucker W, Kumar V, Kandasamy J, Keenan L, Bardarov S, Kriakov J, Lawrence JG, Jacobs WR, Hendrix RW, Hatfull GF (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113(2):171–182

    CAS  CrossRef  PubMed  Google Scholar 

  • Pope WH, Jacobs-Sera D, Russell DA, Rubin DH, Kajee A, Msibi ZN, Larsen MH, Jacobs WR Jr, Lawrence JG, Hendrix RW, Hatfull GF (2014) Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. MBio 5(6):e02145

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  • Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science, Phage Hunters Integrating Research and Education, Mycobacterial Genetics Course (2015) Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife 4:e06416

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • President’s Council of Advisors on Science and Technology (PCAST) (2012) Engage to excel: producing one million additional college graduates with degrees in science, technology, engineering, and mathematics. Executive Office of the President, Washington, DC

    Google Scholar 

  • Rohwer F, Thurber RV (2009) Viruses manipulate the marine environment. Nature 459(7244):207–212

    CAS  CrossRef  PubMed  Google Scholar 

  • Rohwer F, Youle M, Maughan H, Hisakawa N (2014) Life in our phage world: a centennial field guide to the earth’s most diverse inhabitants. Wholon, San Diego

    Google Scholar 

  • Seymour E, Hunter A-B, Laursen SL, DeAntoni T (2004) Establishing the benefits of undergraduate research for undergraduates in the sciences: first findings from a three-year study. Sci Educ 88:493–594

    CrossRef  Google Scholar 

  • Snapper SB, Melton RE, Mustafa S, Kieser T, Jacobs WR Jr (1990) Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol 4(11):1911–1919

    CAS  CrossRef  PubMed  Google Scholar 

Download references

Acknowledgments

I thank Deborah Jacobs-Sera and Welkin Pope for comments on the manuscript. This work was supported by a grant from the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Graham F. Hatfull .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2017 Springer International Publishing AG

About this entry

Cite this entry

Hatfull, G.F. (2017). Bacteriophage Discovery and Genomics. In: Harper, D., Abedon, S., Burrowes, B., McConville, M. (eds) Bacteriophages. Springer, Cham. https://doi.org/10.1007/978-3-319-40598-8_6-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-40598-8_6-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-40598-8

  • Online ISBN: 978-3-319-40598-8

  • eBook Packages: Springer Reference Biomedicine & Life SciencesReference Module Biomedical and Life Sciences