Skip to main content

Advertisement

Log in

Engineering microbes for targeted strikes against human pathogens

  • Review
  • Published:
Cellular and Molecular Life Sciences Aims and scope Submit manuscript

Abstract

Lack of pathogen specificity in antimicrobial therapy causes non-discriminant microbial cell killing that disrupts the microflora present. As a result, potentially helpful microbial cells are killed along with the pathogen, altering the biodiversity and dynamic interactions within the population. Moreover, the unwarranted exposure of antibiotics to microbes increases the likelihood of developing resistance and perpetuates the emergence of multidrug resistance. Synthetic biology offers an alternative solution where specificity can be conferred to reduce the non-specific, non-targeted activity of currently available antibiotics, and instead provides targeted therapy against specific pathogens and minimising collateral damage to the host’s inherent microbiota. With a greater understanding of the microbiome and the available genetic engineering tools for microbial cells, it is possible to devise antimicrobial strategies for novel antimicrobial therapy that are able to precisely and selectively remove infectious pathogens. Herein, we review the strategies developed by unlocking some of the natural mechanisms used by the microbes and how these may be utilised in targeted antimicrobial therapy, with the promise of reducing the current global bane of multidrug antimicrobial resistance.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260–270

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Chen YY, Galloway KE, Smolke CD (2012) Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biol 13:240

    Article  PubMed  PubMed Central  Google Scholar 

  3. Hwang IY, Koh E, Kim HR, Yew WS, Chang MW (2016) Reprogrammable microbial cell-based therapeutics against antibiotic-resistant bacteria. Drug Resist Updates Rev Comment Antimicrob Anticancer Chemother 27:59–71

    Google Scholar 

  4. FDA (2016) Early clinical trials with live biotherapeutic products: chemistry, manufacturing, and control information; guidance for industry

  5. Drider D, Rebuffat S (2011) Prokaryotic antimicrobial peptides: from genes to applications. Springer, New York

    Book  Google Scholar 

  6. Rasamiravaka T, Labtani Q, Duez P, El Jaziri M (2015) The formation of biofilms by Pseudomonas aeruginosa: a review of the natural and synthetic compounds interfering with control mechanisms. Biomed Res Int 2015:759348

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Singh PK, Yadav VK, Kalia M, Dohare S, Sharma D, Agarwal V (2017) Pseudomonas aeruginosa auto inducer 3-oxo-C12-HSL exerts bacteriostatic effect and inhibits Staphylococcus epidermidis biofilm. Microb Pathog 110:612–619

    Article  PubMed  CAS  Google Scholar 

  8. Wang J, Ding L, Li K, Huang H, Hu H, Geng J, Xu K, Ren H (2017) Estimation of spatial distribution of quorum sensing signaling in sequencing batch biofilm reactor (SBBR) biofilms. Sci Total Environ 612:405–414

    Article  PubMed  CAS  Google Scholar 

  9. Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SS, Poh CL, Chang MW (2011) Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol Syst Biol 7:521

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Ling H, Saeidi N, Rasouliha BH, Chang MW (2010) A predicted S-type pyocin shows a bactericidal activity against clinical Pseudomonas aeruginosa isolates through membrane damage. FEBS Lett 584:3354–3358

    Article  PubMed  CAS  Google Scholar 

  11. Gupta S, Bram EE, Weiss R (2013) Genetically programmable pathogen sense and destroy. ACS Synth Biol 2:715–723

    Article  PubMed  CAS  Google Scholar 

  12. Soelaiman S, Jakes K, Wu N, Li C, Shoham M (2001) Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Mol Cell 8:1053–1062

    Article  PubMed  CAS  Google Scholar 

  13. Duport C, Baysse C, Michel-Briand Y (1995) Molecular characterization of pyocin S3, a novel S-type pyocin from Pseudomonas aeruginosa. J Biol Chem 270:8920–8927

    Article  PubMed  CAS  Google Scholar 

  14. Hwang IY, Tan MH, Koh E, Ho CL, Poh CL, Chang MW (2014) Reprogramming microbes to be pathogen-seeking killers. ACS Synth Biol 3:228–237

    Article  PubMed  CAS  Google Scholar 

  15. McKay R, Hauk P, Wu HC, Pottash AE, Shang W, Terrell J, Payne GF, Bentley WE (2017) Controlling localization of Escherichia coli populations using a two-part synthetic motility circuit: an accelerator and brake. Biotechnol Bioeng 114:2883–2895

    Article  PubMed  CAS  Google Scholar 

  16. Hwang IY, Koh E, Wong A, March JC, Bentley WE, Lee YS, Chang MW (2017) Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models. Nat Commun 8:15028

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Holmgren J, Lonnroth I, Mansson J, Svennerholm L (1975) Interaction of cholera toxin and membrane GM1 ganglioside of small intestine. Proc Natl Acad Sci USA 72:2520–2524

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Field M (1971) Intestinal secretion: effect of cyclic AMP and its role in cholera. N Engl J Med 284:1137–1144

    Article  CAS  Google Scholar 

  19. Goodman BE, Percy WH (2005) CFTR in cystic fibrosis and cholera: from membrane transport to clinical practice. Adv Physiol Educ 29:75–82

    Article  PubMed  Google Scholar 

  20. Kelly RC, Bolitho ME, Higgins DA, Lu W, Ng WL, Jeffrey PD, Rabinowitz JD, Semmelhack MF, Hughson FM, Bassler BL (2009) The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA. Nat Chem Biol 5:891–895

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Duan F, March JC (2010) Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc Natl Acad Sci USA 107:11260–11264

    Article  PubMed  PubMed Central  Google Scholar 

  22. Jayaraman P, Holowko MB, Yeoh JW, Lim S, Poh CL (2017) Repurposing a two-component system-based biosensor for the killing of Vibrio cholerae. ACS Synth Biol 6:1403–1415

    Article  PubMed  CAS  Google Scholar 

  23. Borrero J, Chen Y, Dunny GM, Kaznessis YN (2015) Modified lactic acid bacteria detect and inhibit multiresistant enterococci. ACS Synth Biol 4:299–306

    Article  PubMed  CAS  Google Scholar 

  24. Geldart K, Borrero J, Kaznessis YN (2015) Chloride-inducible expression vector for delivery of antimicrobial peptides targeting antibiotic-resistant Enterococcus faecium. Appl Environ Microbiol 81:3889–3897

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Palmer JD, Piattelli E, McCormick BA, Silby MW, Brigham CJ, Bucci V (2017) Engineered probiotic for the inhibition of Salmonella via tetrathionate-induced production of microcin H47. ACS Infect Dis 4:39–45

    Article  PubMed  CAS  Google Scholar 

  26. Gengenbacher M, Kaufmann SHE (2012) Mycobacterium tuberculosis: success through dormancy. FEMS Microbiol Rev 36:514–532

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Atanaskovic I, Bencherif AC, Deyell M, Jaramillo-Riveri S, Benony M, Bernheim AG, Libis VK, Koutsoubelis N, Zegman Y, Lochner AC, Basier C, Aghoghogbe I, Marinkovic ZS, Zahra S, Toulouze M, Lindner AB, Wintermute EH (2014) In situ characterization of mycobacterial growth inhibition by lytic enzymes expressed in vectorized E. coli. ACS Synth Biol 3:932–934

    Article  PubMed  CAS  Google Scholar 

  28. Yang Y, Kulka K, Montelaro RC, Reinhart TA, Sissons J, Aderem A, Ojha AK (2014) A hydrolase of trehalose dimycolate induces nutrient influx and stress sensitivity to balance intracellular growth of Mycobacterium tuberculosis. Cell Host Microbe 15:153–163

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Beauregard KE, Lee KD, Collier RJ, Swanson JA (1997) pH-dependent perforation of macrophage phagosomes by listeriolysin O from Listeria monocytogenes. J Exp Med 186:1159–1163

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Wittebole X, De Roock S, Opal SM (2014) A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens. Virulence 5:226–235

    Article  PubMed  Google Scholar 

  31. Abedon ST, Kuhl SJ, Blasdel BG, Kutter EM (2011) Phage treatment of human infections. Bacteriophage 1:66–85

    Article  PubMed  PubMed Central  Google Scholar 

  32. Lang AS, Zhaxybayeva O, Beatty JT (2012) Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 10:472–482

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Haaber J, Leisner JJ, Cohn MT, Catalan-Moreno A, Nielsen JB, Westh H, Penades JR, Ingmer H (2016) Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells. Nat Commun 7:13333

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Tong SY, Davis JS, Eichenberger E, Holland TL, Fowler VG Jr (2015) Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clin Microbiol Rev 28:603–661

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Capparelli R, Parlato M, Borriello G, Salvatore P, Iannelli D (2007) Experimental phage therapy against Staphylococcus aureus in mice. Antimicrob Agents Chemother 51:2765–2773

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Yilmaz C, Colak M, Yilmaz BC, Ersoz G, Kutateladze M, Gozlugol M (2013) Bacteriophage therapy in implant-related infections: an experimental study. J Bone Jt Surg Am 95:117–125

    Article  Google Scholar 

  37. Sunagar R, Patil SA, Chandrakanth RK (2010) Bacteriophage therapy for Staphylococcus aureus bacteremia in streptozotocin-induced diabetic mice. Res Microbiol 161:854–860

    Article  PubMed  Google Scholar 

  38. Zhang W, Mi Z, Yin X, Fan H, An X, Zhang Z, Chen J, Tong Y (2013) Characterization of Enterococcus faecalis phage IME-EF1 and its endolysin. PLoS ONE 8:e80435

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Khalifa L, Brosh Y, Gelman D, Coppenhagen-Glazer S, Beyth S, Poradosu-Cohen R, Que YA, Beyth N, Hazan R (2015) Targeting Enterococcus faecalis biofilms with phage therapy. Appl Environ Microbiol 81:2696–2705

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Cheng M, Liang J, Zhang Y, Hu L, Gong P, Cai R, Zhang L, Zhang H, Ge J, Ji Y, Guo Z, Feng X, Sun C, Yang Y, Lei L, Han W, Gu J (2017) The bacteriophage EF-P29 efficiently protects against lethal vancomycin-resistant Enterococcus faecalis and alleviates gut microbiota imbalance in a murine bacteremia model. Front Microbiol 8:837

    Article  PubMed  PubMed Central  Google Scholar 

  41. Debarbieux L, Leduc D, Maura D, Morello E, Criscuolo A, Grossi O, Balloy V, Touqui L (2010) Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections. J Infect Dis 201:1096–1104

    Article  PubMed  CAS  Google Scholar 

  42. Alemayehu D, Casey PG, McAuliffe O, Guinane CM, Martin JG, Shanahan F, Coffey A, Ross RP, Hill C (2012) Bacteriophages phiMR299-2 and phiNH-4 can eliminate Pseudomonas aeruginosa in the murine lung and on cystic fibrosis lung airway cells. MBio 3:e00029-00012

    Article  CAS  Google Scholar 

  43. Pabary R, Singh C, Morales S, Bush A, Alshafi K, Bilton D, Alton EW, Smithyman A, Davies JC (2016) Antipseudomonal bacteriophage reduces infective burden and inflammatory response in murine lung. Antimicrob Agents Chemother 60:744–751

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Darch SE, Kragh KN, BAbbott EA, Bjarnsholt T, Bull JJ, Whiteley M (2017) Phage inhibit pathogen dissemination by targeting bacterial migrants in chronic infection model. MBio 8

  45. Fu W, Forster T, Mayer O, Curtin JJ, Lehman SM, Donlan RM (2010) Bacteriophage cocktail for the prevention of biofilm formation by Pseudomonas aeruginosa on catheters in an in vitro model system. Antimicrob Agents Chemother 54:397–404

    Article  PubMed  CAS  Google Scholar 

  46. Kumari S, Harjai K, Chhibber S (2011) Bacteriophage versus antimicrobial agents for the treatment of murine burn wound infection caused by Klebsiella pneumoniae B5055. J Med Microbiol 60:205–210

    Article  PubMed  Google Scholar 

  47. Chadha P, Katare OP, Chhibber S (2017) Liposome loaded phage cocktail: enhanced therapeutic potential in resolving Klebsiella pneumoniae mediated burn wound infections. Burns 43:1532–1543

    Article  PubMed  Google Scholar 

  48. Maura D, Morello E, du Merle L, Bomme P, Le Bouguenec C, Debarbieux L (2012) Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice. Environ Microbiol 14:1844–1854

    Article  PubMed  CAS  Google Scholar 

  49. Galtier M, De Sordi L, Maura D, Arachchi H, Volant S, Dillies MA, Debarbieux L (2016) Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition. Environ Microbiol 18:2237–2245

    Article  PubMed  CAS  Google Scholar 

  50. Galtier M, De Sordi L, Sivignon A, de Vallee A, Maura D, Neut C, Rahmouni O, Wannerberger K, Darfeuille-Michaud A, Desreumaux P, Barnich N, Debarbieux L (2017) Bacteriophages targeting adherent invasive Escherichia coli strains as a promising new treatment for Crohn’s disease. J Crohns Colitis 11:840–847

    PubMed  Google Scholar 

  51. Mai V, Ukhanova M, Reinhard MK, Li M, Sulakvelidze A (2015) Bacteriophage administration significantly reduces Shigella colonization and shedding by Shigella-challenged mice without deleterious side effects and distortions in the gut microbiota. Bacteriophage 5:e1088124

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Regeimbal JM, Jacobs AC, Corey BW, Henry MS, Thompson MG, Pavlicek RL, Quinones J, Hannah RM, Ghebremedhin M, Crane NJ, Zurawski DV, Teneza-Mora NC, Biswas B, Hall ER (2016) Personalized therapeutic cocktail of wild environmental phages rescues mice from Acinetobacter baumannii wound infections. Antimicrob Agents Chemother 60:5806–5816

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Fong SA, Drilling A, Morales S, Cornet ME, Woodworth BA, Fokkens WJ, Psaltis AJ, Vreugde S, Wormald PJ (2017) Activity of bacteriophages in removing biofilms of Pseudomonas aeruginosa isolates from chronic rhinosinusitis patients. Front Cell Infect Microbiol 7:418

    Article  PubMed  PubMed Central  Google Scholar 

  54. Jaiswal A, Koley H, Ghosh A, Palit A, Sarkar B (2013) Efficacy of cocktail phage therapy in treating Vibrio cholerae infection in rabbit model. Microbes Infect 15:152–156

    Article  PubMed  Google Scholar 

  55. Sarker SA, Berger B, Deng Y, Kieser S, Foata F, Moine D, Descombes P, Sultana S, Huq S, Bardhan PK, Vuillet V, Praplan F, Brussow H (2017) Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh. Environ Microbiol 19:237–250

    Article  PubMed  CAS  Google Scholar 

  56. Mirzaei MK, Maurice CF (2017) Menage a trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol 15:397–408

    Article  PubMed  CAS  Google Scholar 

  57. Lu TK, Collins JJ (2009) Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. PNAS 106:4629–4634

    Article  PubMed  PubMed Central  Google Scholar 

  58. Lu TK, Collins JJ (2007) Dispersing biofilms with engineered enzymatic bacteriophage. PNAS 104:11197–11202

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  59. Pei R, Lamas-Samanamud GR (2014) Inhibition of biofilm formation by T7 bacteriophages producing quorum-quenching enzymes. Appl Environ Microbiol 80:5340–5348

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. Ando H, Lemire S, Pires DP, Lu TK (2015) Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst 1:187–196

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  61. Yosef I, Goren MG, Globus R, Molshanski-Mor S, Qimron U (2017) Extending the host range of bacteriophage particles for DNA transduction. Mol Cell 66(721–728):e723

    Google Scholar 

  62. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero AA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712

    Article  PubMed  CAS  Google Scholar 

  63. Le S, Yao X, Lu S, Tan Y, Rao X, Li M, Jin X, Wang J, Zhao Y, Wu NC, Lux R, He X, Shi W, Hu F (2014) Chromosomal DNA deletion confers phage resistance to Pseudomonas aeruginosa. Sci Rep 4:4738

    Article  PubMed  PubMed Central  Google Scholar 

  64. Duerkop BA, Huo W, Bhardwaj P, Palmer KL, Hooper LV (2016) Molecular basis for lytic bacteriophage resistance in Enterococci. MBio 7

  65. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8:317–327

    Article  PubMed  CAS  Google Scholar 

  66. Lu TK, Koeris MS (2011) The next generation of bacteriophage therapy. Curr Opin Microbiol 14:524–531

    Article  PubMed  Google Scholar 

  67. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821

    Article  PubMed  CAS  Google Scholar 

  68. Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR–Cas9 for genome engineering. Cell 157:1262–1278

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  69. Sander JD, Joung JK (2014) CRISPR–Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–355

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR–Cas systems. Nat Biotechnol 31:233–239

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  71. Bikard D, Hatoum-Aslan A, Mucida D, Marraffini LA (2012) CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12:177–186

    Article  PubMed  CAS  Google Scholar 

  72. Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL (2014) Programmable removal of bacterial strains by use of genome-targeting CRISPR–Cas systems. MBio 5:e00928-00913

    Article  CAS  Google Scholar 

  73. Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti VA, Marraffini LA (2014) Exploiting CRISPR–Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 32:1146–1150

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  74. Citorik RJ, Mimee M, Lu TK (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol 32:1141–1145

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  75. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR (2009) Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 53:5046–5054

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Edgar R, Friedman N, Molshanski-Mor S, Qimron U (2012) Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl Environ Microbiol 78:744–751

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  77. Yosef I, Manor M, Kiro R, Qimron U (2015) Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci USA 112:7267–7272

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Park JY, Moon BY, Park JW, Thornton JA, Park YH, Seo KS (2017) Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus. Sci Rep 7:44929

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. Liao HK, Gu Y, Diaz A, Marlett J, Takahashi Y, Li M, Suzuki K, Xu R, Hishida T, Chang CJ, Esteban CR, Young J, Izpisua Belmonte JC (2015) Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat Commun 6:6413

    Article  PubMed  CAS  Google Scholar 

  80. Ramanan V, Shlomai A, Cox DB, Schwartz RE, Michailidis E, Bhatta A, Scott DA, Zhang F, Rice CM, Bhatia SN (2015) CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus. Sci Rep 5:10833

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  81. Yuen KS, Chan CP, Wong NH, Ho CH, Ho TH, Lei T, Deng W, Tsao SW, Chen H, Kok KH, Jin DY (2015) CRISPR/Cas9-mediated genome editing of Epstein-Barr virus in human cells. J Gen Virol 96:626–636

    Article  PubMed  CAS  Google Scholar 

  82. Kennedy EM, Kornepati AV, Goldstein M, Bogerd HP, Poling BC, Whisnant AW, Kastan MB, Cullen BR (2014) Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells by using a bacterial CRISPR/Cas RNA-guided endonuclease. J Virol 88:11965–11972

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Khosravi A, Mazmanian SK (2013) Disruption of the gut microbiome as a risk factor for microbial infections. Curr Opin Microbiol 16:221–227

    Article  PubMed  PubMed Central  Google Scholar 

  84. Harris VC, Haak BW, Boele van Hensbroek M, Wiersinga WJ (2017) The intestinal microbiome in infectious diseases: the clinical relevance of a rapidly emerging field. Open Forum Infect Dis 4:144

    Google Scholar 

  85. Kamada N, Chen GY, Inohara N, Nunez G (2013) Control of pathogens and pathobionts by the gut microbiota. Nat Immunol 14:685–690

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  86. Hardy H, Harris J, Lyon E, Beal J, Foey AD (2013) Probiotics, prebiotics and immunomodulation of gut mucosal defences: homeostasis and immunopathology. Nutrients 5:1869–1912

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Rea MC, Sit CS, Clayton E, O’Connor PM, Whittal RM, Zheng J, Vederas JC, Ross RP, Hill C (2010) Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile. Proc Natl Acad Sci USA 107:9352–9357

    Article  PubMed  PubMed Central  Google Scholar 

  88. van den Elsen LW, Poyntz HC, Weyrich LS, Young W, Forbes-Blom EE (2017) Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases. Clin Transl Immunol 6:e125

    Article  CAS  Google Scholar 

  89. Culligan EP, Sleator RD (2016) Advances in the microbiome: applications to Clostridium difficile infection. J Clin Med 5

  90. Li YT, Cai HF, Wang ZH, Xu J, Fang JY (2016) Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection. Aliment Pharmacol Ther 43:445–457

    Article  PubMed  Google Scholar 

  91. Khoruts A, Sadowsky MJ (2016) Understanding the mechanisms of faecal microbiota transplantation. Nat Rev Gastroenterol Hepatol 13:508–516

    Article  PubMed  PubMed Central  Google Scholar 

  92. Khanna S, Pardi DS, Kelly CR, Kraft CS, Dhere T, Henn MR, Lombardo MJ, Vulic M, Ohsumi T, Winkler J, Pindar C, McGovern BH, Pomerantz RJ, Aunins JG, Cook DN, Hohmann EL (2016) A novel microbiome therapeutic increases gut microbial diversity and prevents recurrent Clostridium difficile infection. J Infect Dis 214:173–181

    Article  PubMed  Google Scholar 

  93. Gerding DN, Meyer T, Lee C, Cohen SH, Murthy UK, Poirier A, Van Schooneveld TC, Pardi DS, Ramos A, Barron MA, Chen H, Villano S (2015) Administration of spores of nontoxigenic Clostridium difficile strain M3 for prevention of recurrent C. difficile infection: a randomized clinical trial. JAMA 313:1719–1727

    Article  PubMed  Google Scholar 

  94. Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, Brown EM, Schroeter K, Allen-Vercoe E (2013) Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome 1:3

    Article  PubMed  PubMed Central  Google Scholar 

  95. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross JR, Toussaint NC, Xavier JB, Pamer EG (2015) Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517:205–208

    Article  PubMed  CAS  Google Scholar 

  96. Lau CS, Chamberlain RS (2016) Probiotics are effective at preventing Clostridium difficile-associated diarrhea: a systematic review and meta-analysis. Int J Gen Med 9:27–37

    PubMed  PubMed Central  Google Scholar 

  97. Shornikova AV, Casas IA, Mykkanen H, Salo E, Vesikari T (1997) Bacteriotherapy with Lactobacillus reuteri in rotavirus gastroenteritis. Pediatr Infect Dis J 16:1103–1107

    Article  PubMed  CAS  Google Scholar 

  98. Ogawa M, Shimizu K, Nomoto K, Takahashi M, Watanuki M, Tanaka R, Tanaka T, Hamabata T, Yamasaki S, Takeda Y (2001) Protective effect of Lactobacillus casei strain Shirota on Shiga toxin-producing Escherichia coli O157:H7 infection in infant rabbits. Infect Immun 69:1101–1108

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  99. Casey PG, Gardiner GE, Casey G, Bradshaw B, Lawlor PG, Lynch PB, Leonard FC, Stanton C, Ross RP, Fitzgerald GF, Hill C (2007) A five-strain probiotic combination reduces pathogen shedding and alleviates disease signs in pigs challenged with Salmonella enterica Serovar Typhimurium. Appl Environ Microbiol 73:1858–1863

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  100. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 103:732–737

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Khosravi Y, Dieye Y, Loke MF, Goh KL, Vadivelu J (2014) Streptococcus mitis induces conversion of Helicobacter pylori to coccoid cells during co-culture in vitro. PLoS ONE 9:e112214

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  102. Zhang M-M, Qian W, Qin Y-Y, He J, Zhou Y-H (2015) Probiotics in Helicobacter pylori eradication therapy: a systematic review and meta-analysis. World J Gastroenterol WJG 21:4345–4357

    Article  PubMed  Google Scholar 

  103. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JFWM, Tijssen JGP, Speelman P, Dijkgraaf MGW, Keller JJ (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 368:407–415

    Article  PubMed  CAS  Google Scholar 

  104. Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, Deakin LJ, Pickard DJ, Duncan SH, Flint HJ, Clark TG, Parkhill J, Dougan G (2012) Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8:e1002995

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  105. Yang YJ, Sheu BS (2012) Probiotics-containing yogurts suppress Helicobacter pylori load and modify immune response and intestinal microbiota in the Helicobacter pylori-infected children. Helicobacter 17:297–304

    Article  PubMed  CAS  Google Scholar 

  106. Wang ZH, Gao QY, Fang JY (2013) Meta-analysis of the efficacy and safety of Lactobacillus-containing and Bifidobacterium-containing probiotic compound preparation in Helicobacter pylori eradication therapy. J Clin Gastroenterol 47:25–32

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the Summit Research Program of the National University Health System (NUHSRO/2016/053/SRP/05), the Synthetic Biology Initiative of the National University of Singapore (DPRT/943/09/14), the U.S. Defense Threat Reduction Agency (HDTRA1-13-0037) and the Ministry of Defence of Singapore (MINDEF, RE2016-074). We thank Dr. Ping Han for her comments on the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Matthew Wook Chang.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hwang, I.Y., Lee, H.L., Huang, J.G. et al. Engineering microbes for targeted strikes against human pathogens. Cell. Mol. Life Sci. 75, 2719–2733 (2018). https://doi.org/10.1007/s00018-018-2827-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00018-018-2827-7

Keywords

Navigation