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Biomedical Journal
Volume 29, Issue 6 (11-2025)
IBJ 2025, 29(6): 374-383 |
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Boogari M, Mohebbi M, Hadidi N. Genetically Engineered Probiotics: Design, Therapeutics, and Clinical Translation. IBJ 2025; 29 (6) :374-383
URL: http://ibj.pasteur.ac.ir/article-1-5197-en.html
URL: http://ibj.pasteur.ac.ir/article-1-5197-en.html
Abstract:
Genetically engineered probiotics (GEPs) aim to address transient colonization and the intra- and inter-subject variability that limit conventional probiotics. These strains utilize Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas editing, programmable gene circuits, and biosensors in chassis such as E. coli Nissle 1917 and L. lactis. This narrative review summarizes the current engineering toolkits and standards (e.g., SEVA), chassis selection criteria, biocontainment strategies, and translational requirements under CMC/GMP frameworks and discusses regulatory considerations for clinical translation. Representative examples include IL-10-secreting Lactococcus lactis and phenylalanine-metabolizing strains for phenylketonuria (SYNB1618/SYNB1934), which illustrate pharmacodynamic target engagement and short-term preclinical safety. We outline clinical advancements in predefined pharmacodynamics, durability of function, monitoring shedding, and horizontal gene transfer, and genomic-microbiome-informed patient stratification. Systems modeling approaches (Genome-Scale Metabolic Model/ Agent-Based Model) are discussed as tools to guide rational design. GEPs offer programmable “sense-and-respond” therapeutics, with successful clinical adoption depending on durable efficacy, long-term safety, and clearly defined regulatory pathways.
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References
1. Huang Y, Zhou Y, Xu H. Unlocking wellness: Probiotics as key drivers in functional food innovation and health promotion. Appl Sci. 2025;15(12):6498. [DOI:10.3390/app15126498]
2. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016;535(7610):94-103 [DOI:10.1038/nature18850]
3. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-36. [DOI:10.1042/BCJ20160510]
4. Hadidi N, Saffari M, Faizi M. Optimized transferosomal bovine lactoferrin (BLF) as a promising novel non-invasive topical treatment for genital warts caused by human papillomavirus (HPV). Iran J Pharm Res. 2018;17(Suppl2):12-23
5. Suez J, Zmora N, Segal E, Elinav E. The pros, cons, and many unknowns of probiotics. Nat Med. 2019;25(5):716-29. [DOI:10.1038/s41591-019-0439-x]
6. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789-99. [DOI:10.1016/j.cell.2014.09.053]
7. Riglar DT, Silver PA. Engineering bacteria for diagnostic and therapeutic applications. Nat Rev Microbiol. 2018;16(4):214-25. [DOI:10.1038/nrmicro.2017.172]
8. Mimee M, Tucker AC, Voigt CA, Lu TK. Programming a human commensal bacterium, bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Syst. 2015;1(1):62-71. [DOI:10.1016/j.cels.2015.06.001]
9. Isabella VM, Ha BN, Castillo MJ, Lubkowicz DJ, Rowe SE, Millet YA, et al. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat Biotechnol. 2018;36(9):857-64. [DOI:10.1038/nbt.4222]
10. Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, et al. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet. 2021;53(2):156-65. [DOI:10.1038/s41588-020-00763-1]
11. Wacklin P, Mäkivuokko H, Alakulppi N, Nikkilä J, Tenkanen H, Räbinä J, et al. Secretor genotype (FUT2 gene) is strongly associated with the composition of Bifidobacteria in the human intestine. Plos One. 2011;6(5):e20113. [DOI:10.1371/journal.pone.0020113]
12. Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, et al. Host genetic variation impacts microbiome composition across human body sites. Genome Biol. 2015;16(1):191. [DOI:10.1186/s13059-015-0759-1]
13. Charbonneau MR, Isabella VM, Li N, Kurtz CB. Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat Commun. 2020;11(1):1738. [DOI:10.1038/s41467-020-15508-1]
14. mora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174(6):1388-405. [DOI:10.1016/j.cell.2018.08.041]
15. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 2013;41(15):7429-37. [DOI:10.1093/nar/gkt520]
16. Liu Y, Wan X, Wang B. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat Commun. 2019;10(1):3693. [DOI:10.1038/s41467-019-11479-0]
17. Rahmati R, Zarimeidani F, Ghanbari Boroujeni MR, Sadighbathi S, Kashaniasl Z, Saleh M, et al. CRISPR-assisted probiotic and in situ engineering of gut microbiota: A prospect to modification of metabolic disorders. Probiotics Antimicrob Proteins. 2025; doi: 10.1007/s12602-025-10561-y. [DOI:10.1007/s12602-025-10561-y]
18. Barra M, Danino T, Garrido D. Engineered probiotics for detection and treatment of inflammatory intestinal diseases. Front Bioeng Biotechnol. 2020;8:265. [DOI:10.3389/fbioe.2020.00265]
19. Stirling F, Bitzan L, O'Keefe S, Redfield E, Oliver JWK, Way J, et al. Rational design of evolutionarily stable microbial kill switches. Mol Cell. 2017;68(4):686-97. [DOI:10.1016/j.molcel.2017.10.033]
20. Silva-Rocha R, Martínez-García E, Calles B, Chavarría M, Arce-Rodríguez A, de Las Heras A, et al. The standard European vector architecture (SEVA): A coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res. 2013;41(Database issue):D666-75. [DOI:10.1093/nar/gks1119]
21. Campos GM, Américo MF, Santos Freitas AD, Barroso FAL, da Cruz Ferraz Dutra J, Quaresma LS, et al. Lactococcus lactis as an interleukin delivery system for prophylaxis and treatment of inflammatory and autoimmune diseases. Probiotics Antimicrob Proteins. 2024;16(2):352-66. [DOI:10.1007/s12602-023-10041-1]
22. Gérard C, Vidal H. Impact of gut microbiota on host glycemic control. Front Endocrinol. 2019;10:29. [DOI:10.3389/fendo.2019.00029]
23. Nagpal R, Wang S, Ahmadi S, Hayes J, Gagliano J, Subashchandrabose S, et al. Human-origin probiotic cocktail increases short-chain fatty acid production via modulation of mice and human gut microbiome. Sci Rep. 2018;8(1):12649. [DOI:10.1038/s41598-018-30114-4]
24. Thorakkattu P, Khanashyam AC, Shah K, Babu KS, Mundanat AS, Deliephan A, et al. Postbiotics: Current trends in food and pharmaceutical industry. Foods. 2022;11(19):3094. [DOI:10.3390/foods11193094]
25. Kamble NS, Thomas S, Madaan T, Ehsani N, Sange S, Tucker K, et al. Engineered bacteria as an orally administered anti-viral treatment and immunization system. Gut Microbes. 2025;17(1):2500056. [DOI:10.1080/19490976.2025.2500056]
26. Aggarwal N, Breedon AME, Davis CM, Hwang IY, Chang MW. Engineering probiotics for therapeutic applications: Recent examples and translational outlook. Curr Opin Biotechnol. 2020;65:171-9. [DOI:10.1016/j.copbio.2020.02.016]
27. LeCureux JS, Dean GA. Lactobacillus mucosal vaccine vectors: Immune responses against bacterial and viral antigens. mSphere. 2018;3(3):e00061-18. [DOI:10.1128/mSphere.00061-18]
28. Mazhar SF, Afzal M, Almatroudi A, Munir S, Ashfaq UA, Rasool M, et al. The prospects for the therapeutic implications of genetically engineered probiotics. J Food Qual. 2020;2020(1):1-11. [DOI:10.1155/2020/9676452]
29. Ma J, Lyu Y, Liu X, Jia X, Cui F, Wu X, et al. Engineered probiotics. Microb Cell Fact. 2022;21(1):72. [DOI:10.1186/s12934-022-01799-0]
30. Bober JR, Beisel CL, Nair NU. Synthetic biology approaches to engineer probiotics and members of the human microbiota for biomedical applications. Annu Rev Biomed Eng. 2018;20:277-300. [DOI:10.1146/annurev-bioeng-062117-121019]
31. He R, Cao Q, Chen J, Tian J. Perspectives on the management of synthetic biological and gene edited foods. Biosaf Health. 2020;2(4):193-8. [DOI:10.1016/j.bsheal.2020.07.003]
32. Stirling F, Silver PA. Controlling the implementation of transgenic microbes: Are we ready for what synthetic biology has to offer? Mol Cell. 2020;78(4):614-23. [DOI:10.1016/j.molcel.2020.03.034]
33. Nazir A, Hussain FHN, Raza A. Advancing microbiota therapeutics: The role of synthetic biology in engineering microbial communities for precision medicine. Front Bioeng Biotechnol. 2024;12:1511149. [DOI:10.3389/fbioe.2024.1511149]
34. Lentzos F. Mutational technologies: Engage public in gene-editing policy. Nature. 2015;521(7552):289. [DOI:10.1038/521289a]
35. Omer R, Mohsin MZ, Mohsin A, Mushtaq BS, Huang X, Guo M, et al. Engineered bacteria-based living materials for biotherapeutic applications. Front Bioeng Biotechnol. 2022;10:870675. [DOI:10.3389/fbioe.2022.870675]
36. Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014;15(2):107-20. [DOI:10.1038/nrg3643]
37. Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2017;35(1):81-9. [DOI:10.1038/nbt.3703]
38. Zomorrodi AR, Segrè D. Synthetic ecology of microbes: Mathematical models and applications. J Mol Biol. 2016;428(5 Pt B):837-61. [DOI:10.1016/j.jmb.2015.10.019]
39. Carr PA, Church GM. Genome engineering. Nat Biotechnol. 2009;27(12):1151-62. [DOI:10.1038/nbt.1590]
40. Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ. Next-generation machine learning for biological networks. Cell. 2018;173(7):1581-92. [DOI:10.1016/j.cell.2018.05.015]
41. Braat H, Rottiers P, Hommes DW, Huyghebaert N, Remaut E, Remon JP, et al. A phase I trial with transgenic bacteria expressing interleukin-10 in Crohn's disease. Clin Gastroenterol Hepatol. 2006;4(6):754-9. [DOI:10.1016/j.cgh.2006.03.028]
42. Cordaillat-Simmons M, Rouanet A, Pot B. Live biotherapeutic products: The importance of a defined regulatory framework. Exp Mol Med. 2020;52(9):1397-406. [DOI:10.1038/s12276-020-0437-6]
43. Ma Z, Zuo T, Frey N, Rangrez AY. A systematic framework for understanding the microbiome in human health and disease: From basic principles to clinical translation. Signal Transduct Target Ther. 2024;9(1):237. [DOI:10.1038/s41392-024-01946-6]
44. Leventhal DS, Sokolovska A, Li N, Plescia C, Kolodziej SA, Gallant CW, et al. Immunotherapy with engineered bacteria by targeting the STING pathway for anti-tumor immunity. Nat Commun. 2020;11(1):2739. [DOI:10.1038/s41467-020-16602-0]
45. Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: Engineering habitats for modular consortia. J Appl Microbiol. 2024;135(7):158. [DOI:10.1093/jambio/lxae158]
46. Pan S, Hsu JC, Hung K-T, Ho C-J. Regulatory framework and challenges for live biotherapeutic products in Taiwan. J Food Drug Anal. 2025;33(2):97-105. [DOI:10.38212/2224-6614.3540]
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