Research progress and medical applications of material-functionalized phages
With the escalating crisis of antimicrobial resistance, the slow pace of traditional antibiotic development presents a critical and growing threat to global public health. Phage therapy, which offers benefits such as high specificity, self-replication, and minimal disruption to the microbiota, has emerged as a promising treatment option. However, its therapeutic potential faces several hurdles, including a limited antibacterial spectrum, inadequate in vivo efficacy, susceptibility to immune clearance, and inability to target intracellular bacteria and biofilm-associated infections. To overcome these issues, new delivery systems have been developed by combining engineered phages with functional materials, such as nanomaterials, hydrogels, and liposomes. This approach significantly improves phage targeting, stability, drug delivery capacity, and controlled release. Nevertheless, engineered phages face challenges such as complex host interactions and intestinal delivery. Future research should incorporate artificial intelligence-assisted design, cross-disciplinary teamwork, and innovative materials to develop phage delivery systems as groundbreaking tools against drug-resistant infections and complex diseases. This review discusses the potential uses of engineered phages in combination with antibiotic therapy, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein gene editing, innovative smart drug delivery, and tumor immune environment control. It also examines the key challenges in translating laboratory studies to clinical use, including technical issues, immune response regulation, and safety concerns.
- Chandrasekhar D, Joseph CM, Parambil JC, et al. Superbugs: An invicible threat in post antibiotic era. Clin Epidemiol Glob Health. 2024;28:101499. doi: 10.1016/j.cegh.2023.101499
- Bayda S, Adeel M, Tuccinardi T, Cordani M, Rizzolio F. The History of Nanoscience and Nanotechnology: From Chemical-Physical Applications to Nanomedicine. Molecules. 2019;25(1):112. doi: 10.3390/molecules25010112
- Kumar M, Parkhey P, Mishra SK, et al. Phage for drug delivery vehicles. Prog Mol Biol Transl Sci. 2023;201:191- 201. doi: 10.1016/bs.pmbts.2023.04.008
- Yao M, Zhu Y, Duan JA, Xiao P. Phage therapy: A novel approach to combat drug-resistant pathogens. Microbiol Res. 2025;298:128228. doi: 10.1016/j.micres.2025.128228
- Lin J, Du F, Long M, Li P. Limitations of Phage Therapy and Corresponding Optimization Strategies: A Review. Molecules. 2022;27(6). doi: 10.3390/molecules27061857
- Wang K, Zhang W, Huang Y, Zhang L, Lou CJSBJ. Application of phage therapy in the treatment of intracellular pathogens. Synth Biol J. 2023;4(4):676. doi: 10.12211/2096-8280.2023-002
- Sahoo K, Meshram S. The Evolution of Phage Therapy: A Comprehensive Review of Current Applications and Future Innovations. Cureus. 2024;16(9):e70414. doi: 10.7759/cureus.70414
- Vila M, Balcão LMN, Balcão VM. Phage Delivery Strategies for Biocontrolling Human, Animal, and Plant Bacterial Infections: State of the Art. Pharmaceutics. 2024;16(3):374. doi: 10.3390/pharmaceutics16030374
- Manohar P, Madurantakam Royam M, Loh B, et al. Synergistic Effects of Phage-Antibiotic Combinations against Citrobacter amalonaticus. ACS Infect Dis. 2022;8(1):59-65. doi: 10.1021/acsinfecdis.1c00117
- Liu H, Li H, Liang Y, et al. Phage-delivered sensitisation with subsequent antibiotic treatment reveals sustained effect against antimicrobial resistant bacteria. Theranostics. 2020;10(14):6310-6321. doi: 10.7150/thno.42573
- Malik DJ, Sokolov IJ, Vinner GK, et al. Formulation, stabilisation and encapsulation of bacteriophage for phage therapy. Adv Colloid Interface Sci. 2017;249:100-133. doi: 10.1016/j.cis.2017.05.014
- Cao Y, Jiang A, Gao Q, Xiao B. Nanocoated bacterial carriers enhance oral bacteriophage delivery efficiency. Acta Pharm Sin B. 2025;15(8):4319-4321. doi: 10.1016/j.apsb.2025.05.037
- Zhao X, Zhong X, Yang S, et al. Guiding antibiotics towards their target using bacteriophage proteins. Nat Commun. 2024;15(1):5287. doi: 10.1038/s41467-024-49603-4
- Hosoya H, Dobroff AS, Driessen WH, et al. Integrated nanotechnology platform for tumor-targeted multimodal imaging and therapeutic cargo release. Proc Natl Acad Sci USA. 2016;113(7):1877-1882. doi: 10.1073/pnas.1525796113
- Dunne M, Rupf B, Tala M, et al. Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Rep. 2019;29(5):1336-1350.e4. doi: 10.1016/j.celrep.2019.09.062
- Ju Z, Sun W. Drug delivery vectors based on filamentous bacteriophages and phage-mimetic nanoparticles. Drug Deliv. 2017;24(1):1898-1908. doi: 10.1080/10717544.2017.1410259
- Hayes WK, Gren ECK, Nelsen DR, et al. It’s a Small World After All: The Remarkable but Overlooked Diversity of Venomous Organisms, with Candidates Among Plants, Fungi, Protists, Bacteria, and Viruses. Toxins. 2025;17(3). doi: 10.3390/toxins17030099
- Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol. 2023;14:1264877. doi: 10.3389/fmicb.2023.1264877
- Mattenberger Y, Knyazhanskaya ES, Shneider MM, et al. The spike tip protein of bacteriophage T4. bioRxiv. 2025. doi: 10.1101/2025.08.28.672839
- Nagakubo T, Nishiyama T, Yamamoto T, et al. Contractile injection systems facilitate sporogenic differentiation of Streptomyces davawensis through the action of a phage tapemeasure protein-related effector. Nat Commun. 2024;15(1):4442. doi: 10.1038/s41467-024-48834-9
- Petrovic Fabijan A, Lin RCY, Ho J, et al. Safety of bacteriophage therapy in severe Staphylococcus aureus infection. Nat Microbiol. 2020;5(3):465-472. doi: 10.1038/s41564-019-0634-z
- Xu J, Ericson CF, Lien YW, et al. Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol. 2022;7(3):397-410. doi: 10.1038/s41564-022-01059-2
- Freeman KG, Mondal S, Macale LS, et al. Structure and infection dynamics of mycobacteriophage Bxb1. Cell. 2025;188(11):2925-2942.e17. doi: 10.1016/j.cell.2025.03.027
- Jing G, Bin X, Xiaokui G, Jinhong Q, Infections. Biological characterization and genome sequence of KP002, a novel bacteriophage isolated from multiple-drug resistant Klebsiella pneumonia. J Microbes Infect. 2016;11(1):18-23
- Li S, Wu J, Wang Q, et al. The landscape of bacterial contractile injection systems across large-scale metagenomes. Microbiol Spectr. 2025;13(7):e0321324. doi: 10.1128/spectrum.03213-24
- Lin L. The expanding universe of contractile injection systems in bacteria. Curr Opin Microbiol. 2024;79:102465. doi: 10.1016/j.mib.2024.102465
- Casu B, Sallmen JW, Haas PE, et al. Function and firing of the Streptomyces coelicolor contractile injection system requires the membrane protein CisA. eLife. 2025;14. doi: 10.7554/eLife.104064
- Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell. 2023;186(1):17-31. doi: 10.1016/j.cell.2022.11.017
- Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs. 2021;35(3):255-280. doi: 10.1007/s40259-021-00480-z
- Nagakubo T. Biological Functions and Applications of Virus-Related Bacterial Nanoparticles: A Review. Int J Mol Sci. 2022;23(5). doi: 10.3390/ijms23052595
- Yamashita W, Chihara K, Azam AH, et al. Phage engineering to overcome bacterial Tmn immunity in Dhillonvirus. Commun Biol. 2025;8(1):290. doi: 10.1038/s42003-025-07730-8
- Marín-Arraiza L, Roa-Eguiara A, Pape T, et al. Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states. Nat Commun. 2025;16(1):9327. doi: 10.1038/s41467-025-64377-z
- Li F, Yu Z-x, Zhang M, et al. Progress in research on bacteriophage receptor-binding proteins and host range extension. Food Sci. 2023;44(23):252-260. doi: 10.7506/spkx1002-6630-20221203-03134
- Brödel AK, Charpenay LH, Galtier M, et al. In situ targeted base editing of bacteria in the mouse gut. Nature. 2024;632(8026):877-884. doi: 10.1038/s41586-024-07681-w
- Yang F, Wang L, Zhou J, et al. In Situ Structures of the Ultra- Long Extended and Contracted Tail of Myoviridae Phage P1. Viruses. 2023;15(6). doi: 10.3390/v15061267
- Yuan S, Shi J, Jiang J, Ma Y. Genome-scale top-down strategy to generate viable genome-reduced phages. Nucleic Acids Res. 2022;50(22):13183-13197. doi: 10.1093/nar/gkac1168
- Sun A, Li CP, Chen Z, et al. The compact Casπ (Cas12l) ‘bracelet’ provides a unique structural platform for DNA manipulation. Cell Res. 2023;33(3):229-244. doi: 10.1038/s41422-022-00771-2
- Zhou J, Wang L, Xiao H, et al. In situ structures of the contractile nanomachine myophage Mu in both its extended and contracted states. J Virol. 2025;99(3):e0205624. doi: 10.1128/jvi.02056-24
- Santos Apolonio J, Lima de Souza Gonçalves V, Cordeiro Santos ML, et al. Oncolytic virus therapy in cancer: A current review. World J Virol. 2021;10(5):229-255. doi: 10.5501/wjv.v10.i5.229
- Roberts A, Adler BA, Cress BF, et al. Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing. Proc Natl Acad Sci U S A. 2025;122(30):e2504853122. doi: 10.1073/pnas.2504853122
- Park JY, Moon BY, Park JW, et al. Genetic engineering of a temperate phage-based delivery system for CRISPR/ Cas9 antimicrobials against Staphylococcus aureus. Sci Rep. 2017;7:44929. doi: 10.1038/srep44929
- Nittayasut N, Yata T, Chirakul S, et al. Non-replicative phage particles delivering CRISPR-Cas9 to target major blaCTX-M variants. PLoS ONE. 2024;19(5):e0303555. doi: 10.1371/journal.pone.0303555
- Yang Y, Du H, Zou G, et al. Encapsulation and delivery of phage as a novel method for gut flora manipulation in situ: A review. J Control Release. 2023;353:634-649. doi: 10.1016/j.jconrel.2022.11.048
- Wang Z, Fokine A, Guo X, et al. Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine. Viruses. 2023;15(8):1673. doi: 10.3390/v15081673
- Nagakubo T, Asamizu S, Yamamoto T, et al. Intracellular Phage Tail-Like Nanostructures Affect Susceptibility of Streptomyces lividans to Osmotic Stress. mSphere. 2023;8(3):e0011423. doi: 10.1128/msphere.00114-23
- Sen A, Nakamura T, Tarashi G, et al. Divergence of an extracellular contractile injection system infectivity elucidated by high resolution structural studies of its tail-baseplate complex. bioRxiv. 2025. doi: 10.1101/2025.07.21.665459
- Peng H, Chen IA, Qimron U. Engineering Phages to Fight Multidrug-Resistant Bacteria. Chem Rev. 2025;125(2):933- 971. doi: 10.1021/acs.chemrev.4c00681
- Wilson JS, Fortier LC, Fagan RP, Bullough PA. Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage. Life Sci Alliance. 2025;8(6):e202403088. doi: 10.26508/lsa.202403088
- Nethery MA, Hidalgo-Cantabrana C, Roberts A, Barrangou R. CRISPR-based engineering of phages for in situ bacterial base editing. Proc Natl Acad Sci USA. 2022;119(46):e2206744119. doi: 10.1073/pnas.2206744119
- Chen Q, Tong YJ. Merging the frontiers: synthetic biology for advanced bacteriophage design. Synth Biol J. 2023;4(2):283. doi: 10.12211/2096-8280.2022-070
- Meeske AJ, Jia N, Cassel AK, et al. A phage-encoded anti- CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Science. 2020;369(6499):54-59. doi: 10.1126/science.abb6151
- Hampton HG, Watson BNJ, Fineran PC. The arms race between bacteria and their phage foes. Nature. 2020;577(7790):327-336. doi: 10.1038/s41586-019-1894-8
- Jia H-J, Jia P-P, Yin S, et al. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Front Microbiol. 2023;14. doi: 10.3389/fmicb.2023.1172635
- Zhang J, He X. Living Bacteriophage Engineering for Functional Material Synthesis, Bioanalytical Sensing and Disease Theranostics. Targets. 2024;2(3):157-185. doi: 10.3390/targets2030010
- Abedon ST. Phage Therapy: Combating Evolution of Bacterial Resistance to Phages. Viruses. 2025;17(8):1094. doi: 10.3390/v17081094
- Evseev P, Shneider M, Miroshnikov K. Evolution of Phage Tail Sheath Protein. Viruses. 2022;14(6):1148. doi: 10.3390/v14061148
- Yoo MK, Kang SK, Choi JH, et al. Targeted delivery of chitosan nanoparticles to Peyer’s patch using M cell-homing peptide selected by phage display technique. Biomaterials. 2010;31(30):7738-7747. doi: 10.1016/j.biomaterials.2010.06.059
- Pardo-Freire M, Domingo-Calap P. Phages and Nanotechnology: New Insights against Multidrug-Resistant Bacteria. Biodes Res. 2023;5:0004. doi: 10.34133/bdr.0004
- Toyonaga N, Mahadevan L. Structural dynamics of contractile injection systems. Biophys J. 2025;124(1):172- 178. doi: 10.1016/j.bpj.2024.11.019
- Mayorga-Ramos A, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. Bacteriophage-mediated approaches for biofilm control. Front Cell Infect Microbiol. 2024;14:1428637. doi: 10.3389/fcimb.2024.1428637
- Emencheta SC, Onugwu AL, Kalu CF, et al. Bacteriophages as nanocarriers for targeted drug delivery and enhanced therapeutic effects. Mater Adv. 2024;5(3):986-1016. doi: 10.1039/d3ma00817g
- Freeman KG, Robotham AC, Parks OB, et al. Virion glycosylation influences mycobacteriophage immune recognition. Cell Host Microbe. 2023;31(7):1216-1231.e6. doi: 10.1016/j.chom.2023.05.028
- Szabó TG, Palotai R, Antal P, et al. Critical role of glycosylation in determining the length and structure of T cell epitopes. Immunome Res. 2009;5(1):4. doi: 10.1186/1745-7580-5-4
- Kim KP, Cha JD, Jang EH, et al. PEGylation of bacteriophages increases blood circulation time and reduces T-helper type 1 immune response. Microb Biotechnol. 2008;1(3):247-257. doi: 10.1111/j.1751-7915.2008.00028.x
- Chitboonthavisuk C, Luo CH, Huss P, et al. Engineering a Dynamic Controllable Infectivity Switch in Bacteriophage T7. ACS Synth Biol. 2022;11(1):286-296. doi: 10.1021/acssynbio.1c00414
- Washizaki A, Sakiyama A, Ando H. Phage-specific antibodies: are they a hurdle for the success of phage therapy? Essays Biochem. 2024;68(5):633-644. doi: 10.1042/ebc20240024
- Weiss GL, Eisenstein F, Kieninger AK, et al. Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria. Nat Microbiol. 2022;7(3):386- 396. doi: 10.1038/s41564-021-01055-y
- Kim SG, Giri SS, Jo SJ, et al. Prolongation of Fate of Bacteriophages In Vivo by Polylactic-Co-Glycolic- Acid/Alginate-Composite Encapsulation. Antibiotics. 2022;11(9):1264. doi: 10.3390/antibiotics11091264
- Hou X, Zhai L, Fu L, et al. Advances in Engineered Phages for Disease Treatment. Small Methods. 2025;9(5):e2401611. doi: 10.1002/smtd.202401611
- Doud MB, Robertson JM, Strathdee SA. Optimizing phage therapy with artificial intelligence: a perspective. Front Cell Infect Microbiol. 2025;15. doi: 10.3389/fcimb.2025.1611857
- Bojar D, Camacho DM, Collins JJJCSHLP. Using Natural Language Processing to Learn the Grammar of Glycans. bioRxiv 2020. doi: 10.1101/2020.01.10.902114
- Nikolic N, Anagnostidis V, Tiwari A, et al. Investigating bacteria-phage interaction dynamics using droplet-based technology. bioRxiv 2023. doi: 10.1101/2023.07.14.549014
- Dąbrowska K, Abedon ST. Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies. Microbiol Mol Biol Rev. 2019;83(4). doi: 10.1128/mmbr.00012-19
- Faltus T, Willy C. Phage therapy-fighting bacteria with viruses. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2025;68(6):581-583. doi: 10.1007/s00103-025-04064-y
- Setegne MT, Cabral AT, Tiwari A, et al. Engineering Cell- Specific Protein Delivery Vehicles for Erythroid Lineage Cells. ACS Bio Med Chem Au. 2025;5(2):268-282. doi: 10.1021/acsbiomedchemau.4c00098
- Peng H, Borg RE, Dow LP, et al. Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages. Proc Natl Acad Sci USA. 2020;117(4):1951-1961. doi: 10.1073/pnas.1913234117
- Tao S, Hu A, Bavel E, et al. Bio-Responsive Hydrogel for Targeted on-Demand Release of a Phage Cocktail for Treatment of Pseudomonas aeruginosa Infection. Adv Funct Mater. 2025;36(2):e09360. doi: 10.1002/adfm.202509360
- Wang Y, Zhang X, Feng X, et al. Purification of Photorhabdus Virulence Cassette (PVC) Protein Complexes from Escherichia coli for Artificial Translocation of Heterologous Cargo Proteins. Bio Protoc. 2024;14(7):e4966. doi: 10.21769/BioProtoc.4966
- Wu W, Hsiao SC, Carrico ZM, Francis MB. Genome-free viral capsids as multivalent carriers for taxol delivery. Angew Chem Int Ed Engl. 2009;48(50):9493-9497. doi: 10.1002/anie.200902426
- Kreitz J, Friedrich MJ, Guru A, et al. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023;616(7956):357-364. doi: 10.1038/s41586-023-05870-7
- Kaur S, Kumari A, Kumari Negi A, et al. Nanotechnology Based Approaches in Phage Therapy: Overcoming the Pharmacological Barriers. Front Pharmacol. 2021;12:699054. doi: 10.3389/fphar.2021.699054
- Chadha P, Katare OP, Chhibber S. Liposome loaded phage cocktail: Enhanced therapeutic potential in resolving Klebsiella pneumoniae mediated burn wound infections. Burns. 2017;43(7):1532-1543. doi: 10.1016/j.burns.2017.03.029
- Abdo GG, Zagho MM, Khalil A. Recent advances in stimuli-responsive drug release and targeting concepts using mesoporous silica nanoparticles. Emerg Mater. 2020;3(3):407-425. doi: 10.1007/s42247-020-00109-x
- Geller LT, Barzily-Rokni M, Danino T, et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science. 2017;357(6356):1156-1160. doi: 10.1126/science.aah5043
- Armstrong H, Bording-Jorgensen M, Dijk S, Wine E. The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It. Cancers. 2018;10(3):83. doi: 10.3390/cancers10030086
- Federici S, Kredo-Russo S, Valdés-Mas R, et al. Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation. Cell. 2022;185(16):2879-2898.e24. doi: 10.1016/j.cell.2022.07.003
- Zachs T, Malit JJL, Xu J, et al. Archaeal type six secretion system mediates contact-dependent antagonism. Sci Adv. 2024;10(46):eadp7088. doi: 10.1126/sciadv.adp7088
- Liu Z, Gray BD, Barber C, et al. Characterization of TCP-1 probes for molecular imaging of colon cancer. J Control Release. 2016;239:223-230. doi: 10.1016/j.jconrel.2016.08.033
- Sales-Dias J, Ferreira A, Lamy M, et al. Development of antibodies against the notch ligand Delta-Like-1 by phage display with activity against breast cancer cells. N Biotechnol. 2021;64:17-26. doi: 10.1016/j.nbt.2021.05.003
- Kang K, Kim K, Lee SR, et al. Selection and Characterization of YKL-40-Targeting Monoclonal Antibodies from Human Synthetic Fab Phage Display Libraries. Int J Mol Sci. 2020;21(17):6354. doi: 10.3390/ijms21176354
- Sung TY, Huang HL, Cheng CC, et al. EGFL6 promotes colorectal cancer cell growth and mobility and the anti-cancer property of anti-EGFL6 antibody. Cell Biosci. 2021;11(1):53. doi: 10.1186/s13578-021-00561-0
- Yu X, Long Y, Chen B, et al. PD-L1/TLR7 dual-targeting nanobody-drug conjugate mediates potent tumor regression via elevating tumor immunogenicity in a host-expressed PD-L1 bias-dependent way. J Immunother Cancer. 2022;10(10):e004590. doi: 10.1136/jitc-2022-004590
