Targeted Probiotic Delivery via Bacteriophage-Resistant Capsules: A Novel Approach to Enhance Gut Health Review Article

Main Article Content

Mehwish Nisar
Amber Nawab
Khurram Rafiq Ahmed
Marium Mumtaz
Sidra Siddiqui
Saria Tariq

Abstract

Probiotics are live microorganisms that have beneficial health effects when taken. Because they may be harmed by gastrointestinal tract disorders, beneficial bacteria must be delivered through effective mechanisms in order to maximize their potential. By using bacteriophage-resistant capsules for targeted probiotic delivery, the study aims to investigate a novel approach to enhancing gut health. The review investigates how combining bacteriophage-resistant capsules with different encapsulation techniques can improve the survivability, specificity, and efficacy of probiotics in the GI tract. The study looks at phage-resistant capsules, complex interactions between phages and probiotics, and various encapsulation methods for bacteriophages and probiotics, including hydrogels, spray drying, liposomes, and microencapsulation. It concludes that by combining advanced encapsulation techniques with bacteriophage-resistant capsules, R-capsule technology can alter microbiota, treat illness, improve nutritional outcomes, extend the shelf life of probiotics, and create customized gut health regimens.

Article Details

Section

Review Article

How to Cite

Targeted Probiotic Delivery via Bacteriophage-Resistant Capsules: A Novel Approach to Enhance Gut Health: Review Article. (2025). Pak-Euro Journal of Medical and Life Sciences, 8(3), 535-556. https://doi.org/10.31580/pjmls.v8i3.3389

References

1. Verna EC, Lucak SJTaig. Use of probiotics in gastrointestinal disorders: what to recommend? Therapeutic Advances in Gastroenterology. 2010;3(5):307-19.

2. Govender M, Choonara YE, Kumar P, du Toit LC, van Vuuren S, Pillay VJAP. A review of the advancements in probiotic delivery: Conventional vs. non-conventional formulations for intestinal flora supplementation. AAPS PharmSciTech. 2014;15:29-43.

3. Li C, Wang ZX, Xiao H, Wu FGJAM. Intestinal delivery of probiotics: materials, strategies, and applications Advanced Materials. 2024;36(32):2310174.

4. Wang Z-D, Zhang W, Liang T-XJP. Advancements in Oral Delivery Systems for Probiotics Based on Polysaccharides. Polymers.2025;17(2):144.

5. Wolfe W, Xiang Z, Yu X, Li P, Chen H, Yao M, et al. The challenge of applications of probiotics in gastrointestinal diseases. Advanced Gut & Microbiome Research. 2023;2023(1):1984200.

6. Sultana K, Godward G, Reynolds N, Arumugaswamy R, Peiris P, Kailasapathy KJIjofm. Encapsulation of probiotic bacteria with alginate–starch and evaluation of survival in simulated gastrointestinal conditions and in yoghurt. International Journal of Food Microbiology. 2000;62(1-2):47-55.

7. Pereira EPR, da Graça JS, Ferreira BM, Balthazar CF, Xavier-Santos D, Bezerril FF, et al. What are the main obstacles to turning foods healthier through probiotics incorporation? a review of functionalization of foods by probiotics and bioactive metabolites. Food Research International. 2024;176:113785.

8. Loh B, Gondil VS, Manohar P, Khan FM, Yang H, Leptihn SJA, et al. Encapsulation and delivery of therapeutic phages. Applied and Environmental Microbiology. 2021;87(5):e01979-20.

9. Loh B, Gondil V, Manohar P, Khan F, Yang H, Leptihn S. Encapsulation and Delivery of Therapeutic Phages. Applied and Environmental Microbiology. 2020;87.

10. Batalha LS, Gontijo MTP, De Carvalho Teixeira AVN, Boggione DMG, Lopez MS, Eller MR, et al. Encapsulation in alginate-polymers improves stability and allows controlled release of the UFV-AREG1 bacteriophage. Food research international. 2021;139:109947.

11. Cortés P, Cano-Sarabia M, Colom J, Otero J, Maspoch D, Llagostera M. Nano/microformulations for Bacteriophage Delivery. Methods in molecular biology. 2024;2734:117-30.

12. Otero J, García-Rodríguez A, Cano-Sarabia M, Maspoch D, Marcos R, Cortés P, et al. Biodistribution of Liposome-Encapsulated Bacteriophages and Their Transcytosis During Oral Phage Therapy. Frontiers in Microbiology. 2019;10.

13. Malik D. Bacteriophage Encapsulation Using Spray Drying for Phage Therapy. Current issues in molecular biology. 2020;40:303-16.

14. Chang R, Wong J, Mathai A, Morales S, Kutter E, Britton W, et al. Production of highly stable spray dried phage formulations for treatment of Pseudomonas aeruginosa lung infection. European Journal of Pharmaceutics and Biopharmaceutics. 2017;121:1.

15. Vinner G, Rezaie-Yazdi Z, Leppanen M, Stapley A, Leaper M, Malik D. Microencapsulation of Salmonella-Specific Bacteriophage Felix O1 Using Spray-Drying in a pH-Responsive Formulation and Direct Compression Tableting of Powders into a Solid Oral Dosage Form. Pharmaceuticals. 2019;12.

16. Leung S, Parumasivam T, Gao F, Carrigy N, Vehring R, Finlay W, et al. Production of Inhalation Phage Powders Using Spray Freeze Drying and Spray Drying Techniques for Treatment of Respiratory Infections. Pharmaceutical Research. 2016;33:1486-96.

17. Yan W, He R, Tang X, Tian B, Liu Y, Tong Y, et al. The Influence of Formulation Components and Environmental Humidity on Spray-Dried Phage Powders for Treatment of Respiratory Infections Caused by Acinetobacter baumannii. Pharmaceutics. 2021;13.

18. Leung S, Parumasivam T, Gao F, Carter E, Carrigy N, Vehring R, et al. Effects of storage conditions on the stability of spray dried, inhalable bacteriophage powders. International journal of pharmaceutics. 2017;521 1-2:141-9.

19. Leung S, Parumasivam T, Nguyen A, Gengenbach T, Carter E, Carrigy N, et al. Effect of storage temperature on the stability of spray dried bacteriophage powders. European Journal of Pharmaceutics and Biopharmaceutics. 2018;127:213.

20. Ergin F. Effect of freeze drying, spray drying and electrospraying on the morphological, thermal, and structural properties of powders containing phage Felix O1 and activity of phage Felix O1 during storage. Powder Technology. 2022.

21. Vandenheuvel D, Singh A, Vandersteegen K, Klumpp J, Lavigne R, Van den Mooter G. Feasibility of spray drying bacteriophages into respirable powders to combat pulmonary bacterial infections. European Journal of Pharmaceutics and Biopharmaceutics. 2013;84(3):578-82.

22. Vanić Ž, Jøraholmen MW, Škalko-Basnet N. Challenges and considerations in liposomal hydrogels for the treatment of infection. Expert Opinion on Drug Delivery. 2025;22:255-76.

23. Gao W, Vecchio D, Li J, Zhu J, Zhang Q, Fu V, et al. Hydrogel Containing Nanoparticle-Stabilized Liposomes for Topical Antimicrobial Delivery. ACS Nano. 2014;8:2900-7.

24. Yang P, Li J, Xiumei, Hu N, Song Z, Chen B, et al. Novel delivery systems for phages and lysins in the topical management of wound infections: a narrative review. Frontiers in Microbiology. 2025;16.

25. Elkhoury K, Koçak P, Kang A, Arab-Tehrany E, Ward JE, Shin S. Engineering Smart Targeting Nanovesicles and Their Combination with Hydrogels for Controlled Drug Delivery. Pharmaceutics. 2020;12.

26. Ahmad N, Bukhari SNA, Hussain M, Ejaz H, Munir MU, Amjad MW. Nanoparticles incorporated hydrogels for delivery of antimicrobial agents: developments and trends. RSC Advances. 2024;14:13535-64.

27. Wdowiak M, Paczesny J, Raza SJP. Enhancing the stability of bacteriophages using physical, chemical, and nano-based approaches: A review. 2022;14(9):1936.

28. Binaymotlagh R, Haghighi FH, Chronopoulou L, Palocci C. Liposome–Hydrogel Composites for Controlled Drug Delivery Applications. Gels. 2024;10.

29. Furlani F, Rossi A, Grimaudo M, Bassi G, Giusto E, Molinari F, et al. Controlled Liposome Delivery from Chitosan-Based Thermosensitive Hydrogel for Regenerative Medicine. International Journal of Molecular Sciences. 2022;23.

30. Manohar P, Ramesh N. Improved lyophilization conditions for long-term storage of bacteriophages. Scientific Reports. 2019;9.

31. Zhang Y, Peng X, Zhang H, Watts A, Ghosh D. Manufacturing and ambient stability of shelf freeze dried bacteriophage powder formulations. International Journal of Pharmaceutics. 2018;542:1.

32. Merabishvili M, Vervaet C, Pirnay J, De Vos D, Verbeken G, Mast J, et al. Stability of Staphylococcus aureus Phage ISP after Freeze-Drying (Lyophilization). PLoS ONE. 2013;8.

33. Liang L, Carrigy N, Kariuki S, Muturi P, Onsare R, Nagel T, et al. Development of a Lyophilization Process for Campylobacter Bacteriophage Storage and Transport. Microorganisms. 2020;8.

34. González-Menéndez E, Fernández L, Gutiérrez D, Rodríguez A, Martínez B, García P. Comparative analysis of different preservation techniques for the storage of Staphylococcus phages aimed for the industrial development of phage-based antimicrobial products. PLoS ONE. 2018;13.

35. Śliwka P, Skaradziński G, Dusza I, Grzywacz A, Skaradzińska A. Freeze-Drying of Encapsulated Bacteriophage T4 to Obtain Shelf-Stable Dry Preparations for Oral Application. Pharmaceutics. 2023;15.

36. Puapermpoonsiri U, Ford S, Van Der Walle C. Stabilization of bacteriophage during freeze drying. International journal of pharmaceutics. 2010;389 1-2:168-75.

37. Adali MB, Barresi AA, Boccardo G, Pisano R. Spray freeze-drying as a solution to continuous manufacturing of pharmaceutical products in bulk. Processes. 2020;8(6):709.

38. Ergin F. Effect of freeze drying, spray drying and electrospraying on the morphological, thermal, and structural properties of powders containing phage Felix O1 and activity of phage Felix O1 during storage. Powder Technology. 2022;404:117516.

39. Ji R, Wu J, Zhang J-L, Wang T, Zhang X-D, Shao L, et al. Extending Viability of Bifidobacterium longum in Chitosan-Coated Alginate Microcapsules Using Emulsification and Internal Gelation Encapsulation Technology. Frontiers in Microbiology. 2019;10.

40. Wani S, Ali M, Mehdi S, Masoodi M, Zargar M, Shakeel F. A review on chitosan and alginate-based microcapsules: Mechanism and applications in drug delivery systems. International journal of biological macromolecules. 2023:125875.

41. Călinoiu L, Ștefănescu B, Pop I, Muntean L, Vodnar D. Chitosan Coating Applications in Probiotic Microencapsulation. Coatings. 2019.

42. Rizo-Vázquez F, Vázquez-Ovando A, Mejía-Reyes D, Gálvez-López D, Rosas-Quijano R. Use of Lactulose as Prebiotic and Chitosan Coating for Improvement the Viability of Lactobacillus sp. FM4.C1.2 Microencapsulate with Alginate. Processes. 2024.

43. Parsana Y, Yadav M, Kumar S. Microencapsulation in the chitosan-coated alginate-inulin matrix of Limosilactobacillus reuteri SW23 and Lactobacillus salivarius RBL50 and their characterization. Carbohydrate Polymer Technologies and Applications. 2023.

44. Escobar A, Muzzio N, Moya S. Antibacterial Layer-by-Layer Coatings for Medical Implants. Pharmaceutics. 2020;13.

45. Arnon-Rips H, Poverenov E. Improving food products' quality and storability by using Layer by Layer edible coatings. Trends in Food Science and Technology. 2018;75:81-92.

46. Akkuş-Dağdeviren ZB, Fürst A, Friedl JD, Tribus M, Bernkop‐Schnürch A. Nanoarchitectonics of Layer-by-Layer (LbL) coated nanostructured lipid carriers (NLCs) for Enzyme-Triggered charge reversal. Journal of colloid and interface science. 2022;629 Pt A:541-53.

47. Gnanasampanthan T, Beyer C, Yu W, Karthäuser J, Wanka R, Spöllmann S, et al. Effect of Multilayer Termination on Nonspecific Protein Adsorption and Antifouling Activity of Alginate-Based Layer-by-Layer Coatings. Langmuir : the ACS journal of surfaces and colloids. 2021.

48. Carosio F, Alongi J. Ultra-Fast Layer-by-Layer Approach for Depositing Flame Retardant Coatings on Flexible PU Foams within Seconds. ACS applied materials & interfaces. 2016;8 10:6315-9.

49. Thaher YA, Abdelghany S, Abulateefeh S. pH-responsive LBL coated silica nanocarriers for controlled release of chlorhexidine. Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2023.

50. Soliman WS, Shaapan RM, Mohamed LA, Gayed SSJOvj. Recent biocontrol measures for fish bacterial diseases, in particular to probiotics, bio-encapsulated vaccines, and phage therapy. 2019;9(3):190–5-–5.

51. Patpatia S, Schaedig E, Dirks A, Paasonen L, Skurnik M, Kiljunen SJFiC, et al. Rapid hydrogel-based phage susceptibility test for pathogenic bacteria. 2022;12:1032052.

52. Afzaal M, Saeed F, Ateeq H, Shah YA, Hussain M, Javed A, et al. Effect of cellulose–chitosan hybrid-based encapsulation on the viability and stability of probiotics under simulated gastric transit and in kefir. 2022;7(3):109.

53. Gondil VS, Chhibber SJFiP. Bacteriophage and endolysin encapsulation systems: a promising strategy to improve therapeutic outcomes. 2021;12:675440.

54. Singla S, Harjai K, Katare OP, Chhibber SJPO. Encapsulation of bacteriophage in liposome accentuates its entry in to macrophage and shields it from neutralizing antibodies. 2016;11(4):e0153777.

55. Abdelsattar AS, Nofal R, Makky S, Safwat A, Taha A, El-Shibiny AJA. The synergistic effect of biosynthesized silver nanoparticles and phage zcse2 as a novel approach to combat multidrug-resistant salmonella enterica. 2021;10(6):678.

56. Kim H, Jang JH, Jung IY, Kim HR, Cho JHJB. Novel genetically engineered probiotics for targeted elimination of Pseudomonas aeruginosa in intestinal colonization. 2023;11(10):2645.

57. Vinner G, Vladisavljević G, Clokie M, Malik D. Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release. PLoS ONE. 2017;12.

58. Luong T, Salabarria A-C, Roach D. Phage Therapy in the Resistance Era: Where Do We Stand and Where Are We Going? Clinical therapeutics. 2020.

59. Gutiérrez B, Domingo-Calap P. Phage Therapy in Gastrointestinal Diseases. Microorganisms. 2020;8.

60. Hasan M, Ahn J. Evolutionary Dynamics between Phages and Bacteria as a Possible Approach for Designing Effective Phage Therapies against Antibiotic-Resistant Bacteria. Antibiotics. 2022;11.

61. Yeung TW, Üçok EF, Tiani KA, McClements DJ, Sela DAJFim. Microencapsulation in alginate and chitosan microgels to enhance viability of Bifidobacterium longum for oral delivery. 2016;7:494.

62. Vinceković M, Bandić LM, Oštarić F, Kiš M, Zdolec N, Marić I, et al. Simultaneous Encapsulation of Probiotic Bacteria (Lactococcus lactis, and Lactiplantibacillus plantarum) in Calcium Alginate Hydrogels. 2025;11(1):34.

63. Samedi L, Charles ALJF. Viability of 4 probiotic bacteria microencapsulated with arrowroot starch in the simulated gastrointestinal tract (GIT) and yoghurt. 2019;8(5):175.

64. Massounga Bora AF, Li X, Liu LJF. Physicochemical and functional characterization of newly designed biopolymeric-based encapsulates with probiotic culture and charantin. 2021;10(11):2677.

65. Patarroyo JL, Florez-Rojas JS, Pradilla D, Valderrama-Rincón JD, Cruz JC, Reyes LHJP. Formulation and characterization of gelatin-based hydrogels for the encapsulation of Kluyveromyces lactis—Applications in packed-bed reactors and probiotics delivery in humans. 2020;12(6):1287.

66. Yang A-J, Marito S, Yang J-J, Keshari S, Chew C-H, Chen C-C, et al. A microtube array membrane (MTAM) encapsulated live fermenting Staphylococcus epidermidis as a skin probiotic patch against Cutibacterium acnes. 2018;20(1):14.

67. Stark K, Hitchcock JP, Fiaz A, White AL, Baxter EA, Biggs S, et al. Encapsulation of emulsion droplets with metal shells for subsequent remote, triggered release. 2019;11(13):12272-82.

68. Timilsena YP, Haque MA, Adhikari BJF, Sciences N. Encapsulation in the food industry: A brief historical overview to recent developments. 2020;11(6):481-508.

69. Sun Q, Yin S, He Y, Cao Y, Jiang CJN. Biomaterials and encapsulation techniques for probiotics: Current status and future prospects in biomedical applications. 2023;13(15):2185.

70. Spacova I, Petrova M, Fremau A, Pollaris L, Vanoirbeek J, Ceuppens J, et al. Intranasal administration of probiotic Lactobacillus rhamnosus GG prevents birch pollen‐induced allergic asthma in a murine model. 2019;74(1):100-10.

71. Nagarajan V, Peng M, Tabashsum Z, Salaheen S, Padilla J, Biswas D. Antimicrobial Effect and Probiotic Potential of Phage Resistant Lactobacillus plantarum and its Interactions with Zoonotic Bacterial Pathogens. Foods. 2019;8.

72. Liu CG, Green S, Min L, Clark J, Salazar K, Terwilliger A, et al. Phage-Antibiotic Synergy Is Driven by a Unique Combination of Antibacterial Mechanism of Action and Stoichiometry. mBio. 2020;11.

73. Nagarajan V, Peng M, Tabashsum Z, Salaheen S, Padilla J, Biswas DJF. Antimicrobial effect and probiotic potential of phage resistant Lactobacillus plantarum and its interactions with zoonotic bacterial pathogens. 2019;8(6):194.

74. Shaufi MAM, Sieo CC, Chong CW, Geok Hun T, Omar AR, Han Ming G, et al. Effects of phage cocktail, probiotics, and their combination on growth performance and gut microbiota of broiler chickens. 2023;13(8):1328.

75. Buttimer C, Sutton T, Colom J, Murray E, Bettio PH, Smith L, et al. Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo. 2022;13:936083.

76. Peng M, Tabashsum Z, Anderson M, Truong A, Houser A, Padilla J, et al. Effectiveness of probiotics, prebiotics, and prebiotic-like components in common functional foods. Comprehensive reviews in food science and food safety. 2020;19 4:1908-33.

77. Ashaolu T. Immune boosting functional foods and their mechanisms: A critical evaluation of probiotics and prebiotics. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie. 2020;130:110625.

78. Obayomi OV, Olaniran AF, Owa SO. Unveiling the role of functional foods with emphasis on prebiotics and probiotics in human health: A review. Journal of Functional Foods. 2024.

79. Wang H, Sun Y, Ma X, Yang T, Wang FJN. The lactobacillus plantarum P-8 probiotic microcapsule prevents DSS-induced colitis through improving intestinal integrity and reducing colonic inflammation in mice. 2024;16(7):1055.

80. Jamaledin R, Sartorius R, Di Natale C, Onesto V, Manco R, Mollo V, et al. PLGA microparticle formulations for tunable delivery of a nano-engineered filamentous bacteriophage-based vaccine: in vitro and in silico-supported approach. Journal of Nanostructure in Chemistry. 2023:1-16.

81. Hussain MA, Liu H, Wang Q, Zhong F, Guo Q, Balamurugan SJCrifs, et al. Use of encapsulated bacteriophages to enhance farm to fork food safety. 2017;57(13):2801-10.

82. Tidim G, Guzel M, Soyer Y, Erel-Goktepe I. Layer-by-layer assembly of chitosan/alginate thin films containing Salmonella enterica bacteriophages for antibacterial applications. Carbohydrate polymers. 2023;328:121710.

83. Moura-Alves M, Esteves A, Ciríaco M, Silva J, Saraiva C. Antimicrobial and Antioxidant Edible Films and Coatings in the Shelf-Life Improvement of Chicken Meat. Foods. 2023;12.

84. Kızal B, Ayaz N, Çufaoğlu G, Göncüoğlu M. CONTROL OF SALMONELLA ENTERITIDIS AND SALMONELLA KENTUCKY ON EGGSHELL WITH BACTERIOPHAGE APPLICATION. Journal of Applied Biological Sciences. 2024.

85. Rindhe S, Khan A, Priyadarshi R, Chatli M, Wagh R, Kumbhar V, et al. Application of bacteriophages in biopolymer‐based functional food packaging films. 2024;23(3):e13333.

86. Forsyth J, Barron N, Scott L, Watson B, Chisnall M, Meaden S, et al. Decolonizing drug-resistant E. coli with phage and probiotics: breaking the frequency-dependent dominance of residents. Microbiology. 2023;169.

87. Tóth A, Csabai I, Judge MF, Maróti G, Becsei Á, Spisák S, et al. Mobile Antimicrobial Resistance Genes in Probiotics. Antibiotics. 2021;10.

88. González-Villalobos E, Balcázar J. Does phage-mediated horizontal gene transfer represent an environmental risk? Trends in microbiology. 2022.

89. Daniali M, Nikfar S, Abdollahi M. Antibiotic resistance propagation through probiotics. Expert Opinion on Drug Metabolism & Toxicology. 2020;16:1207-15.

90. Jaglan AB, Anand T, Verma R, Vashisth M, Virmani N, Bera B, et al. Tracking the phage trends: a comprehensive review of applications in therapy and food production. 2022;13:993990.

91. Moye Z, Woolston J, Sulakvelidze A. Bacteriophage Applications for Food Production and Processing. Viruses. 2018;10.

92. Hosseini A, Saba MK, Watkins C. Microbial antagonists to biologically control postharvest decay and preserve fruit quality. Critical Reviews in Food Science and Nutrition. 2023;64:7330-42.

93. Yasmin I, Saeed M, Pasha I, Zia M. Development of Whey Protein Concentrate-Pectin-Alginate Based Delivery System to Improve Survival of B. longum BL-05 in Simulated Gastrointestinal Conditions. Probiotics and Antimicrobial Proteins. 2019;11:413-26.

94. Rojas-Muñoz Y, Santagapita P, Quintanilla‐Carvajal M. Probiotic Encapsulation: Bead Design Improves Bacterial Performance during In Vitro Digestion. Polymers. 2023;15.

95. Abdelkader K, Gutiérrez D, Latka A, Boeckaerts D, Drulis-Kawa Z, Criel B, et al. The Specific Capsule Depolymerase of Phage PMK34 Sensitizes Acinetobacter baumannii to Serum Killing. Antibiotics. 2022;11.

96. Łubkowska B, Czajkowska E, Stodolna A, Sroczynski M, Zylicz-Stachula A, Sobolewski I, et al. A novel thermostable TP-84 capsule depolymerase: a method for rapid polyethyleneimine processing of a bacteriophage-expressed proteins. Microbial Cell Factories. 2023;22.

97. Song L, Yang X, Huang J, Zhu X, Han G, Wan Y, et al. Phage selective pressure reduces virulence of hypervirulent Klebsiella pneumoniae through mutation of the wzc gene. 2021;12:739319.

98. Abuqwider J, Di Porzio A, Barrella V, Gatto C, Sequino G, De Filippis F, et al. Limosilactobacillus reuteri DSM 17938 reverses gut metabolic dysfunction induced by Western diet in adult rats. 2023;10:1236417.

99. Da Silva MN, Tagliapietra B, Flores VDA, Richards NSPDS. In vitro test to evaluate survival in the gastrointestinal tract of commercial probiotics. Current Research in Food Science. 2021;4:320-5.

100. Arnal M, Denis S, Uriot O, Lambert C, Holowacz S, Paul F, et al. Impact of oral galenic formulations of Lactobacillus salivarius on probiotic survival and interactions with microbiota in human in vitro gut models. Beneficial microbes. 2021:1-16.

101. Morelli L, Pellegrino P. A critical evaluation of the factors affecting the survival and persistence of beneficial bacteria in healthy adults. Beneficial microbes. 2021:1-12.

102. Govaert M, Rotsaert C, Vannieuwenhuyse C, Duysburgh C, Medlin S, Marzorati M, et al. Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition. Nutrients. 2024;16.

103. Bernatek M, Żukiewicz-Sobczak W, Lachowicz-Wiśniewska S, Piątek J. Factors Determining Effective Probiotic Activity: Evaluation of Survival and Antibacterial Activity of Selected Probiotic Products Using an “In Vitro” Study. Nutrients. 2022;14.

104. Rajam R, Subramanian P. Encapsulation of probiotics: past, present and future. Beni-Suef University Journal of Basic and Applied Sciences. 2022;11.

105. Rossmann FS, Racek T, Wobser D, Puchalka J, Rabener EM, Reiger M, et al. Phage-mediated dispersal of biofilm and distribution of bacterial virulence genes is induced by quorum sensing. 2015;11(2):e1004653.

106. Ulrich L, Giez C, Steiner LX, Hentschel U, Lachnit TJFiM. Adaptive lifestyle of bacteria determines phage-bacteria interaction. 2022;13:1056388.

107. Yus C, Gracia R, Larrea A, Andreu V, Irusta S, Sebastian V, et al. Targeted release of probiotics from enteric microparticulated formulations. 2019;11(10):1668.

108. Sun Q, Wicker LJF. Hydrogel encapsulation of lactobacillus casei by block charge modified pectin and improved gastric and storage stability. 2021;10(6):1337.

109. Han J, McClements D, Liu X, Liu F. Oral delivery of probiotics using single-cell encapsulation. Comprehensive reviews in food science and food safety. 2024;23 3.

110. Yao M, Xie J, Du H, McClements D, Xiao H, Li L. Progress in microencapsulation of probiotics: A review. Comprehensive reviews in food science and food safety. 2020;19 2:857-74.

111. Vitetta L, Vitetta G, Hall S. Immunological Tolerance and Function: Associations Between Intestinal Bacteria, Probiotics, Prebiotics, and Phages. Frontiers in Immunology. 2018;9.

112. Kim J, Hosseindoust A, Lee S, Choi Y, Kim M, Lee J, et al. Bacteriophage cocktail and multi-strain probiotics in the feed for weanling pigs: effects on intestine morphology and targeted intestinal coliforms and Clostridium. Animal : an international journal of animal bioscience. 2017;11 1:45-53.

113. Neschislyaev V, Shilova E, Nikolaeva A, Orlova E. Study of a combined biological product with antibacterial and probiotic activity. Biological Products Prevention, Diagnosis, Treatment. 2023.

114. Soundararajan M, Von Bünau R, Oelschlaeger T. K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917. Frontiers in Microbiology. 2019;10.

115. Bryan D, El-Shibiny A, Hobbs Z, Porter J, Kutter E. Bacteriophage T4 Infection of Stationary Phase E. coli: Life after Log from a Phage Perspective. Frontiers in Microbiology. 2016;7.

116. Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, et al. Bacterial Retrons Function In Anti-Phage Defense. Cell. 2020;183:1551-61.

117. Gaborieau B, Delattre R, Adiba S, Clermont O, Denamur E, Ricard J, et al. Variable fitness effects of bacteriophage resistance mutations in Escherichia coli: implications for phage therapy. Journal of Virology. 2024;98.

118. Wu Y, Garushyants S, Van Den Hurk A, Aparicio-Maldonado C, Kushwaha S, King C, et al. Bacterial defense systems exhibit synergistic anti-phage activity. Cell host & microbe. 2024.

119. Colom J, Cano-Sarabia M, Otero J, Cortés P, Maspoch D, Llagostera M. Liposome-Encapsulated Bacteriophages for Enhanced Oral Phage Therapy against Salmonella spp. Applied and Environmental Microbiology. 2015;81:4841-9.

120. Wang R, Yeh Y-J, An Y-N, Virly. Engineering pH-sensitive erodible chitosan hydrogel composite containing bacteriophage: An interplay between hydrogel and bacteriophage against Staphylococcus aureus. International journal of biological macromolecules. 2023:127371.

121. Dini C, Islan G, De Urraza P, Castro G. Novel biopolymer matrices for microencapsulation of phages: enhanced protection against acidity and protease activity. Macromolecular bioscience. 2012;12 9:1200-8.

122. Malik D, Sokolov I, Vinner G, Mancuso F, Cinquerrui S, Vladisavljević G, et al. Formulation, stabilisation and encapsulation of bacteriophage for phage therapy. Advances in colloid and interface science. 2017;249:100-33.

123. Soundararajan M, von Bünau R, Oelschlaeger TAJFiM. K5 capsule and lipopolysaccharide are important in resistance to T4 phage attack in probiotic E. coli strain Nissle 1917. 2019;10:2783.

124. Cinquerrui S, Mancuso F, Vladisavljević GT, Bakker SE, Malik DJJFim. Nanoencapsulation of bacteriophages in liposomes prepared using microfluidic hydrodynamic flow focusing. 2018;9:2172.

125. Volodkin D, Petrov A, Prevot M, Sukhorukov G. Matrix polyelectrolyte microcapsules: new system for macromolecule encapsulation. Langmuir : the ACS journal of surfaces and colloids. 2004;20 8:3398-406.

126. Musin EV, Kim AL, Dubrovskii AV, Ariskina EV, Kudryashova EB, Tikhonenko SAJP. The pathways to create containers for bacteriophage delivery. 2022;14(3):613.

127. Wang C, Tang H, Duan Y, Zhang Q, Shan W, Wang X, et al. Oral biomimetic virus vaccine hydrogel for robust abscopal antitumour efficacy. Journal of colloid and interface science. 2024;674:92-107.

128. Yang F, Meng L, Lin S, Wu F, Liu J. Polyethyleneimine-complexed charge-reversed yeast cell walls for the enhanced oral delivery of pseudovirus-based antigens. Chemical communications. 2021.

129. Zhao Z, Qiao S, Jin Z, Li H, Yu H, Zhang C, et al. Acidified sucralfate encapsulated chitosan derivative nanoparticles as oral vaccine adjuvant delivery enhancing mucosal and systemic immunity. International journal of biological macromolecules. 2024:135424.

130. Costa MJ, Pastrana LM, Teixeira JA, Sillankorva SM, Cerqueira MAJV. Bacteriophage delivery systems for food applications: Opportunities and perspectives. 2023;15(6):1271.

131. Zhang C, Gao X, Ren X, Xu T, Peng Q, Zhang Y, et al. Bacteria-Induced Colloidal Encapsulation for Probiotic Oral Delivery. ACS nano. 2023.

132. Xu C, Ban Q, Wang W, Hou J, Jiang Z-M. Novel nano-encapsulated probiotic agents: Encapsulate materials, delivery, and encapsulation systems. Journal of controlled release : official journal of the Controlled Release Society. 2022.

133. Gu Q, Yin Y, Yan X, Liu X, Liu F, McClements D. Encapsulation of multiple probiotics, synbiotics, or nutrabiotics for improved health effects: A review. Advances in colloid and interface science. 2022;309:102781.

134. Altamirano FG, Forsyth J, Patwa R, Kostoulias X, Trim M, Subedi D, et al. Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials. Nature Microbiology. 2021;6:157-61.

135. Rendueles O, De Sousa JM, Rocha E. Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies. eLife. 2023;12.

136. Bai J, Raustad N, Denoncourt J, Van Opijnen T, Geisinger E. Genome-wide phage susceptibility analysis in Acinetobacter baumannii reveals capsule modulation strategies that determine phage infectivity. PLOS Pathogens. 2023;19.

137. Majkowska-Skrobek G, Markwitz P, Sosnowska E, Lood C, Lavigne R, Drulis-Kawa Z. The evolutionary trade-offs in phage-resistant Klebsiella pneumoniae entail cross-phage sensitization and loss of multidrug resistance. Environmental microbiology. 2021.

138. Guglielmotti D, Marcó M, Golowczyc M, Reinheimer J, Quiberoni A. Probiotic potential of Lactobacillus delbrueckii strains and their phage resistant mutants. International Dairy Journal. 2007;17:916-25.

139. Lo Curto A, Pitino I, Mandalari G, Dainty J, Faulks R, Wickham MSJ. Survival of probiotic lactobacilli in the upper gastrointestinal tract using an in vitro gastric model of digestion. Food microbiology. 2011;28 7:1359-66.

140. Gao H, Li, Sun W, McClements D, Cheng C, Zeng H, et al. Impact of encapsulation of probiotics in oil-in-water high internal phase emulsions on their thermostability and gastrointestinal survival. Food Hydrocolloids. 2021.

141. Suvarna S, Dsouza J, Ragavan M, Das N. Potential probiotic characterization and effect of encapsulation of probiotic yeast strains on survival in simulated gastrointestinal tract condition. Food Science and Biotechnology. 2018;27:745-53.

142. Zeashan M, Afzaal M, Saeed F, Ahmed A, Tufail T, Ahmed A, et al. Survival and behavior of free and encapsulated probiotic bacteria under simulated human gastrointestinal and technological conditions. Food Science & Nutrition. 2020;8:2419-26.

143. Gunzburg W, Aung M, Toa P, Ng S, Read E, Tan W, et al. Efficient Protection of Probiotics for Delivery to the Intestinal tract by Cellulose Sulphate Encapsulation. 2020.

144. Foster TJJNrm. Immune evasion by staphylococci. 2005;3(12):948-58.

145. Stummeyer K, Schwarzer D, Claus H, Vogel U, Gerardy‐Schahn R, Mühlenhoff MJMm. Evolution of bacteriophages infecting encapsulated bacteria: lessons from Escherichia coli K1‐specific phages. 2006;60(5):1123-35.

146. Pingoud A, Fuxreiter M, Pingoud V, Wende WJC, sciences ml. Type II restriction endonucleases: structure and mechanism. 2005;62:685-707.

147. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EVJBd. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. 2006;1:1-26.

148. Koonin EV, Makarova KSJPTotRSB. Origins and evolution of CRISPR-Cas systems. 2019;374(1772):20180087.

149. Lopatina A, Tal N, Sorek RJArov. Abortive infection: bacterial suicide as an antiviral immune strategy. 2020;7(1):371-84.

150. Vimon S, Kertsomboon T, Chirachanchai S, Angkanaporn K, Nuengjamnong CJCP. Matrices-charges of agar-alginate crosslinked microcapsules via o/w microemulsion: A non-spore forming probiotic bacteria encapsulation system for extensive viability. 2023;321:121302.

151. Kouamé KJE-P, Bora AFM, Li X, Sun Y, Hussain M, Liu L, et al. Recent Advances for Encapsulating Spore Forming and Non-Spore Forming Probiotic Bacteria: Applications in Functional Food Products. 2022.

152. Dalmasso M, Strain R, Neve H, Franz CM, Cousin FJ, Ross RP, et al. Three new Escherichia coli phages from the human gut show promising potential for phage therapy. 2016;11(6):e0156773.

153. Markwitz P, Olszak T, Gula G, Kowalska M, Arabski M, Drulis-Kawa ZJV. Emerging phage resistance in Pseudomonas aeruginosa PAO1 is accompanied by an enhanced heterogeneity and reduced virulence. 2021;13(7):1332.

154. Kaur S, Harjai K, Chhibber SJPo. In vivo assessment of phage and linezolid based implant coatings for treatment of methicillin resistant S. aureus (MRSA) mediated orthopaedic device related infections. 2016;11(6):e0157626.

155. Nakakido M, Tanaka N, Shimojo A, Miyamae N, Tsumoto KJPo. Development of a high-throughput method to screen novel antiviral materials. 2022;17(4):e0266474.

156. Jovanović M, Petrović M, Miočinović J, Zlatanović S, Laličić Petronijević J, Mitić-Ćulafić D, et al. Bioactivity and sensory properties of probiotic yogurt fortified with apple pomace flour. 2020;9(6):763.

157. Song M-W, Park J-Y, Lee H-S, Kim K-T, Paik H-DJA. Co-fermentation by Lactobacillus brevis B7 improves the antioxidant and immunomodulatory activities of hydroponic ginseng-fortified yogurt. 2021;10(9):1447.

158. Cordeiro BF, Alves JL, Belo GA, Oliveira ER, Braga MP, da Silva SH, et al. Therapeutic effects of probiotic minas frescal cheese on the attenuation of ulcerative colitis in a murine model. 2021;12:623920.

159. Chen L, Wu D, Schlundt J, Conway PLJFim. Development of a dairy-free fermented oat-based beverage with enhanced probiotic and bioactive properties. 2020;11:609734.

160. Gómez-Fernández AR, Faccinetto-Beltrán P, Orozco-Sánchez NE, Pérez-Carrillo E, Marín-Obispo LM, Hernández-Brenes C, et al. Sugar-free milk chocolate as a carrier of omega-3 polyunsaturated fatty acids and probiotics: A potential functional food for the diabetic population. 2021;10(8):1866.

161. Kumari VB C, Huligere SS, Alotaibi G, Al Mouslem AK, Bahauddin AA, Shivanandappa TB, et al. Antidiabetic activity of potential probiotics limosilactobacillus spp., levilactobacillus spp., and lacticaseibacillus spp. isolated from fermented sugarcane juice: a comprehensive in vitro and in silico study. 2023;15(8):1882.

162. D’Alessandro M, Parolin C, Bukvicki D, Siroli L, Vitali B, De Angelis M, et al. Probiotic and metabolic characterization of vaginal lactobacilli for a potential use in functional foods. 2021;9(4):833.

163. Vitellio P, Celano G, Bonfrate L, Gobbetti M, Portincasa P, De Angelis MJN. Effects of Bifidobacterium longum and Lactobacillus rhamnosus on gut microbiota in patients with lactose intolerance and persisting functional gastrointestinal symptoms: A randomised, double-blind, cross-over study. 2019;11(4):886.

164. Ashraf R, Shah N. Immune System Stimulation by Probiotic Microorganisms. Critical Reviews in Food Science and Nutrition. 2014;54:938-56.

165. Mazziotta C, Tognon M, Martini F, Torreggiani E, Rotondo J. Probiotics Mechanism of Action on Immune Cells and Beneficial Effects on Human Health. Cells. 2023;12.

166. Galdeano M, Cazorla S, Dumit JML, Vélez E, Perdigón G. Beneficial Effects of Probiotic Consumption on the Immune System. Annals of Nutrition and Metabolism. 2019;74:115-24.

167. Xu H, Huang W, Hou Q, Kwok L-Y, Laga W, Wang Y, et al. Oral administration of compound probiotics improved canine feed intake, weight gain, immunity and intestinal microbiota. 2019;10:394673.

168. Stacey H, De Soir S, Jones J. The Safety and Efficacy of Phage Therapy: A Systematic Review of Clinical and Safety Trials. Antibiotics. 2022;11.

169. Fabijan AP, Iredell J, Danis-Wlodarczyk K, Kebriaei R, Abedon S. Translating phage therapy into the clinic: Recent accomplishments but continuing challenges. PLOS Biology. 2023;21.

170. Yang Q, Le S, Zhu T, Wu N. Regulations of phage therapy across the world. Frontiers in Microbiology. 2023;14.

171. Collins G, Dhiman P, Jie, Schlussel M, Archer L, Van Calster B, et al. Evaluation of clinical prediction models (part 1): from development to external validation. The BMJ. 2024;384.

172. Zbrozek A, Hebert J, Gogates G, Thorell R, Dell C, Molsen E, et al. Validation of electronic systems to collect patient-reported outcome (PRO) data-recommendations for clinical trial teams: report of the ISPOR ePRO systems validation good research practices task force. Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research. 2013;16 4:480-9.

173. Toll D, Janssen K, Vergouwe Y, Moons K. Validation, updating and impact of clinical prediction rules: a review. Journal of clinical epidemiology. 2008;61 11:1085-94.

174. McMillen C, Doyle A, Claypool E. Validation as a clinical strategy. Journal of Social Work Practice. 2022;37:325-38.

175. Abedon S, Danis-Wlodarczyk K, Wozniak D. Phage Cocktail Development for Bacteriophage Therapy: Toward Improving Spectrum of Activity Breadth and Depth. Pharmaceuticals. 2021;14.

176. Kim MK, Suh G, Cullen G, Rodriguez SP, Dharmaraj T, Chang T, et al. Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches. The Journal of Clinical Investigation. 2025;135.

177. Cha K, Oh HK, Jang JY, Jo Y, Kim WK, Ha GU, et al. Characterization of two novel bacteriophages infecting multidrug-resistant (MDR) Acinetobacter baumannii and evaluation of their therapeutic efficacy in vivo. 2018;9:696.

178. Shibu A, Kurup BM, Harikrishnan M, Boopendranath M. Impact of Climate Change on Hydrological Cycle, Ecosystem, Fisheries and Food Security. England; 2022.