Skip to main content

Isolation and Functional Characterization of Fusobacterium nucleatum Bacteriophage

  • Protocol
  • First Online:
The Oral Microbiome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2327))

Abstract

Bacteriophages are viruses that specifically lyse bacteria. They have demonstrated potential in applications as antibacterial agents in medicine, agriculture, and environmental remediation. Due to the complex and dynamic nature of the oral microbiome, antibiotic treatment of chronic, polymicrobial oral diseases may lead to dysbiosis. In these diseases, bacteriophages may provide targeted activity against oral bacteria without such disruption to the broader microbial community. In this chapter, we describe the methods for screening samples that may contain bacteriophages against oral pathogenic bacteria, and using the example of FNU1, the bacteriophage we isolated against Fusobacterium nucleatum, describe the process of bacteriophage purification and characterization.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Han YW (2015) Fusobacterium nucleatum: a commensal-turned pathogen. Curr Opin Microbiol 23:141–147. https://doi.org/10.1016/j.mib.2014.11.013

    Article  CAS  PubMed  Google Scholar 

  2. Rickard AH, Gilbert P, High NJ, Kolenbrander PE, Handley PS (2003) Bacterial coaggregation: an integral process in the development of multi-species biofilms. Trends Microbiol 11(2):94–100. https://doi.org/10.1016/s0966-842x(02)00034-3

    Article  CAS  PubMed  Google Scholar 

  3. Han YW, Shi W, Huang GT, Kinder Haake S, Park NH, Kuramitsu H et al (2000) Interactions between periodontal bacteria and human oral epithelial cells: fusobacterium nucleatum adheres to and invades epithelial cells. Infect Immun 68(6):3140–3146. https://doi.org/10.1128/iai.68.6.3140-3146.2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Høiby N, Bjarnsholt T, Givskov M, Molin S, Ciofu O (2010) Antibiotic resistance of bacterial biofilms. Int J Antimicrob Agents 35(4):322–332. https://doi.org/10.1016/j.ijantimicag.2009.12.011

    Article  CAS  PubMed  Google Scholar 

  5. Imbuluzqueta E, Gamazo C, Ariza J, Blanco-Prieto MJ (2010) Drug delivery systems for potential treatment of intracellular bacterial infections. Front Biosci (Landmark Ed) 15:397–417. https://doi.org/10.2741/3627

    Article  CAS  Google Scholar 

  6. Kilian M (2018) The oral microbiome - friend or foe? Eur J Oral Sci 126(Suppl 1):5–12. https://doi.org/10.1111/eos.12527

    Article  PubMed  Google Scholar 

  7. Dicks LMT, Mikkelsen LS, Brandsborg E, Marcotte H (2019) Clostridium difficile, the difficult “Kloster” fuelled by antibiotics. Curr Microbiol 76(6):774–782. https://doi.org/10.1007/s00284-018-1543-8

    Article  CAS  PubMed  Google Scholar 

  8. Theochari NA, Stefanopoulos A, Mylonas KS, Economopoulos KP (2018) Antibiotics exposure and risk of inflammatory bowel disease: a systematic review. Scand J Gastroenterol 53(1):1–7. https://doi.org/10.1080/00365521.2017.1386711

    Article  CAS  PubMed  Google Scholar 

  9. Roubaud-Baudron C, Ruiz VE, Swan AM, Vallance BA, Ozkul C, Pei Z et al (2019) Long-term effects of early-life antibiotic exposure on resistance to subsequent bacterial infection. mBio 10(6). https://doi.org/10.1128/mBio.02820-19

  10. Boursi B, Mamtani R, Haynes K, Yang Y (2015) Recurrent antibiotic exposure may promote cancer formation—another step in understanding the role of the human microbiota? Eur J Cancer 51(17):2655–2664. https://doi.org/10.1016/j.ejca.2015.08.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Dodds DR (2017) Antibiotic resistance: a current epilogue. Biochem Pharmacol 134:139–146. https://doi.org/10.1016/j.bcp.2016.12.005

    Article  CAS  PubMed  Google Scholar 

  12. Gordillo Altamirano FL, Barr JJ (2019) Phage therapy in the postantibiotic era. Clin Microbiol Rev 32(2). https://doi.org/10.1128/CMR.00066-18

  13. Vandenheuvel D, Lavigne R, Brussow H (2015) Bacteriophage therapy: advances in formulation strategies and human clinical trials. Annu Rev Virol 2(1):599–618. https://doi.org/10.1146/annurev-virology-100114-054915

    Article  CAS  PubMed  Google Scholar 

  14. Shabbir MA, Hao H, Shabbir MZ, Wu Q, Sattar A, Yuan Z (2016) Bacteria vs. bacteriophages: parallel evolution of immune arsenals. Front Microbiol 7:1292. https://doi.org/10.3389/fmicb.2016.01292

    Article  PubMed  PubMed Central  Google Scholar 

  15. Batinovic S, Wassef F, Knowler SA et al (2019) Bacteriophages in natural and artificial environments. Pathogens 8(3). https://doi.org/10.3390/pathogens8030100

  16. Machuca P, Daille L, Vinés E, Berrocal L, Bittner M (2010) Isolation of a novel bacteriophage specific for the periodontal pathogen Fusobacterium nucleatum. Appl Environ Microbiol 76(21):7243–7250. https://doi.org/10.1128/AEM.01135-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kabwe M, Brown TL, Dashper S, Speirs L, Ku H, Petrovski S et al (2019) Genomic, morphological and functional characterisation of novel bacteriophage FNU1 capable of disrupting Fusobacterium nucleatum biofilms. Sci Rep 9(1):9107. https://doi.org/10.1038/s41598-019-45549-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Khalifa L, Shlezinger M, Beyth S, Houri-Haddad Y, Coppenhagen-Glazer S, Beyth N et al (2016) Phage therapy against Enterococcus faecalis in dental root canals. J Oral Microbiol 8:32157. https://doi.org/10.3402/jom.v8.32157

    Article  PubMed  Google Scholar 

  19. Hillman ET, Lu H, Yao T, Nakatsu C (2017) Microbial ecology along the gastrointestinal tract. Microbes Environ 32(4):300–313. https://doi.org/10.1264/jsme2.ME17017

    Article  PubMed  PubMed Central  Google Scholar 

  20. Zheng DW, Dong X, Pan P, Chen KW, Fan JX, Cheng SX et al (2019) Phage-guided modulation of the gut microbiota of mouse models of colorectal cancer augments their responses to chemotherapy. Nat Biomed Eng 3(9):717–728. https://doi.org/10.1038/s41551-019-0423-2

    Article  CAS  PubMed  Google Scholar 

  21. Schneider C, Zemp E, Zitzmann NU (2019) Dental care behaviour in Switzerland. Swiss Dent J 129(6):466–478

    PubMed  Google Scholar 

  22. Fernandez CE, Fontana M, Samarian D, Cury JA, Rickard AH, González-Cabezas C (2016) Effect of fluoride-containing toothpastes on enamel demineralization and Streptococcus mutans biofilm architecture. Caries Res 50(2):151–158. https://doi.org/10.1159/000444888

    Article  CAS  PubMed  Google Scholar 

  23. Ardizzoni A, Pericolini E, Paulone S, Orsi CF, Castagnoli A, Oliva I et al (2018) In vitro effects of commercial mouthwashes on several virulence traits of Candida albicans, viridans streptococci and Enterococcus faecalis colonizing the oral cavity. PLoS One 13(11):e0207262. https://doi.org/10.1371/journal.pone.0207262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Brown TL, Ku H, Mnatzaganian G, Angove M, Petrovski S, Kabwe M et al (2020) The varying effects of a range of preservatives on Myoviridae and Siphoviridae bacteriophages formulated in a semi-solid cream preparation. Lett Appl Microbiol. https://doi.org/10.1111/lam.13299

  25. Castillo DE, Nanda S, Keri JE (2018) Propionibacterium (Cutibacterium) acnes bacteriophage therapy in acne: current evidence and future perspectives. Dermatol Ther (Heidelb). https://doi.org/10.1007/s13555-018-0275-9

  26. Garretto A, Miller-Ensminger T, Wolfe AJ, Putonti C (2019) Bacteriophages of the lower urinary tract. Nat Rev Urol 16(7):422–32. https://doi.org/10.1038/s41585-019-0192-4

  27. Letkiewicz S, Miedzybrodzki R, Klak M, Jonczyk E, Weber-Dabrowska B, Górski A (2010) The perspectives of the application of phage therapy in chronic bacterial prostatitis. FEMS Immunol Med Microbiol 60(2):99–112. https://doi.org/10.1111/j.1574-695X.2010.00723.x

  28. Chang RYK, Wallin M, Lin Y, Leung SSY, Wang H, Morales S et al (2018) Phage therapy for respiratory infections. Adv Drug Deliv Rev 133:76–86. https://doi.org/10.1016/j.addr.2018.08.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Vazquez R, Garcia E, Garcia P (2018) Phage lysins for fighting bacterial respiratory infections: a new generation of antimicrobials. Front Immunol 9:2252. https://doi.org/10.3389/fimmu.2018.02252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Lopetuso LR, Giorgio ME, Saviano A, Scaldaferri F, Gasbarrini A, Cammarota G (2019) Bacteriocins and bacteriophages: therapeutic weapons for gastrointestinal diseases? Int J Mol Sci 20(1). https://doi.org/10.3390/ijms20010183

  31. Shkoporov AN, Hill C (2019) Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe 25(2):195–209. https://doi.org/10.1016/j.chom.2019.01.017

    Article  CAS  PubMed  Google Scholar 

  32. Shkoporov AN, Khokhlova EV, Fitzgerald CB, Stockdale SR, Draper LA, Ross RP et al (2018) PhiCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat Commun 9(1):4781. https://doi.org/10.1038/s41467-018-07225-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Khan Mirzaei M, Khan MAA, Ghosh P, Taranu ZE, Taguer M, Ru J et al (2020) Bacteriophages isolated from stunted children can regulate gut bacterial communities in an age-specific manner. Cell Host Microbe 27(2):199–212.e5. https://doi.org/10.1016/j.chom.2020.01.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Mitchell HL, Dashper SG, Catmull DV, Paolini RA, Cleal SM, Slakeski N et al (2010) Treponema denticola biofilm-induced expression of a bacteriophage, toxin-antitoxin systems and transposases. Microbiology 156(Pt 3):774–788. https://doi.org/10.1099/mic.0.033654-0

    Article  CAS  PubMed  Google Scholar 

  35. Baker JL, Hendrickson EL, Tang X, Lux R, He X, Edlund A et al (2019) Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota. Proc Natl Acad Sci U S A 116(17):8499–8504. https://doi.org/10.1073/pnas.1820594116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Chen T, Olsen I (2019) Porphyromonas gingivalis and its CRISPR-Cas system. J Oral Microbiol 11(1):1638196. https://doi.org/10.1080/20002297.2019.1638196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. van der Ploeg JR (2009) Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages. Microbiology 155(Pt 6):1966–1976. https://doi.org/10.1099/mic.0.027508-0

    Article  CAS  PubMed  Google Scholar 

  38. Hyman P, Abedon ST (2010) Bacteriophage host range and bacterial resistance. Adv Appl Microbiol 70:217–248. https://doi.org/10.1016/S0065-2164(10)70007-1

    Article  CAS  PubMed  Google Scholar 

  39. Hyman P (2019) Phages for phage therapy: isolation, characterization, and host range breadth. Pharmaceuticals (Basel) 12(1). https://doi.org/10.3390/ph12010035

  40. Branston SD, Wright J, Keshavarz-Moore E (2015) A non-chromatographic method for the removal of endotoxins from bacteriophages. Biotechnol Bioeng 112(8):1714–1719. https://doi.org/10.1002/bit.25571

    Article  CAS  PubMed  Google Scholar 

  41. Ackermann HW, Audurier A, Berthiaume L, Jones LA, Mayo JA, Vidaver AK (1978) Guidelines for bacteriophage characterization. Adv Virus Res 23:1–24. https://doi.org/10.1016/s0065-3527(08)60096-2

    Article  CAS  PubMed  Google Scholar 

  42. Kutter E (2009) Phage host range and efficiency of plating. Methods Mol Biol (Clifton, NJ) 501:141–149. https://doi.org/10.1007/978-1-60327-164-6_14

    Article  CAS  Google Scholar 

  43. Nelson PS, Papas TS, Schweinfest CW (1993) Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios. Nucleic Acids Res 21(3):681–686. https://doi.org/10.1093/nar/21.3.681

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Joseph Tucci .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Kabwe, M., Brown, T., Ku, H., Dashper, S., Tucci, J. (2021). Isolation and Functional Characterization of Fusobacterium nucleatum Bacteriophage. In: Adami, G.R. (eds) The Oral Microbiome. Methods in Molecular Biology, vol 2327. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1518-8_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1518-8_4

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1517-1

  • Online ISBN: 978-1-0716-1518-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics