Nutrition Induced Gut Microbiota Modulation in Food Animals: Implications for Viral Susceptibility, Shedding and Transmission Dynamics for Sustainable Development

Year : 2026 | Volume : 03 | Issue : 01 | Page : 46 56
    By

    Md. Emran Hossain,

  1. Professor, Department of Animal Science and Nutrition, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh, India

Abstract

The gut microbiota has emerged as a central mediator linking host nutrition, immune competence, and vulnerability to viral pathogens in food animals. Diet is a primary driver of microbial community structure and function, influencing metabolite production, intestinal barrier integrity, and systemic antiviral immunity. Accumulating evidence indicates that nutrition induced modulation of the gut microbiota can substantially alter viral susceptibility, replication, and shedding patterns, with downstream effects on transmission dynamics within and between animal populations. This review synthesizes current knowledge on the tripartite interactions among diet, gut microbiota, and viral infections in major food animal species including poultry, swine, and ruminants. It critically evaluates how macronutrients, micronutrients, and functional feed additives shape microbial ecosystems and related immune pathways that govern host responses to viral challenge. Mechanistic insights into microbiota derived metabolites, mucosal immunity, and gut barrier regulation are integrated with empirical findings on viral load, shedding duration, and environmental persistence. The review further explores how nutrition mediated microbial modulation can be strategically leveraged to reduce disease burden, enhance vaccine responsiveness, and improve farm level biosecurity. Key knowledge gaps are identified, particularly the need for longitudinal, multi-omics, and field-based studies that bridge experimental models with commercial production systems. Overall, this synthesis highlights the potential of precision nutrition and microbiota targeted interventions as sustainable tools to mitigate viral risks while supporting productivity, health, and resilience in food animal production systems

Keywords: Animal health, gut microbiota, nutrition, sustainability, viral infection, viral shedding, viral transmission

[This article belongs to International Journal of Virus Studies ]

How to cite this article:
Md. Emran Hossain. Nutrition Induced Gut Microbiota Modulation in Food Animals: Implications for Viral Susceptibility, Shedding and Transmission Dynamics for Sustainable Development. International Journal of Virus Studies. 2026; 03(01):46-56.
How to cite this URL:
Md. Emran Hossain. Nutrition Induced Gut Microbiota Modulation in Food Animals: Implications for Viral Susceptibility, Shedding and Transmission Dynamics for Sustainable Development. International Journal of Virus Studies. 2026; 03(01):46-56. Available from: https://journals.stmjournals.com/ijvs/article=2026/view=237725


References

  1. Obianwuna UE, Agbai Kalu N, Wang J, Zhang H, Qi G, Qiu K, Wu S. Recent trends on mitigative effect of probiotics on oxidative-stress-induced gut dysfunction in broilers under necrotic enteritis challenge: a review. Antioxidants. 2023 Apr 11;12(4):911.
  2. Ali M, Xu C, Wang M, Hina Q, Ji Y, Anwar S, Lu S, He Q, Qiu Y, Li K. Gut barrier dysfunction and microbiota variations in cryptosporidiosis: A comprehensive review. Veterinary Sciences. 2025 Jan 23;12(2):85.
  3. Acharya A, Barsila SR. Exploring alternatives to antibiotics in poultry production: a comprehensive review of emerging strategies and their implications for avian health. World’s Poultry Science Journal. 2025 Oct 2;81(4):1427-60.
  4. Attia YA, Helal IE, Nagadi SA, Khafaga AF, Taha AE, Asiry KA, Abdulsalam NM, Zabermawi NM, Shafi ME, Zakaria HA, Ebeid TA. Gut dysbiosis: causes and prevention Strategies–A review. Annals of Animal Science. 2025 Oct 24;25(4):1297-311.
  5. Zhang Y, Ma Y, Qi Y. Potential relationship between gut microbiota and animal diarrhea: a systematic review. Frontiers in Microbiology. 2025 Jul 24;16:1637331.
  6. El-Khoury G, Hajjar C, Geitani R, Karam Sarkis D, Butel MJ, Barbut F, Abifadel M, Kapel N. Gut microbiota and viral respiratory infections: microbial alterations, immune modulation, and impact on disease severity: a narrative review. Frontiers in Microbiology. 2025 Jul 18;16:1605143.
  7. Asumang P, Ntumi R, Dwomoh F. Unveiling microbial dynamics: a review of health and immune enhancement in school settings. Frontiers in Microbiomes. 2024 Dec 4;3:1488702.
  8. Kempf F, La Ragione R, Chirullo B, Schouler C, Velge P. Super shedding in enteric pathogens: a review. Microorganisms. 2022 Oct 22;10(11):2101.
  9. Omatola CA, Olaniran AO. Rotaviruses: From pathogenesis to disease control—A critical review. Viruses. 2022 Apr 22;14(5):875.
  10. Sorboni SG, Moghaddam HS, Jafarzadeh-Esfehani R, Soleimanpour S. A comprehensive review on the role of the gut microbiome in human neurological disorders. Clinical microbiology reviews. 2022 Jan 19;35(1):e00338-20.
  11. Aldars-García L, Marin AC, Chaparro M, Gisbert JP. The interplay between immune system and microbiota in inflammatory bowel disease: a narrative review. International journal of molecular sciences. 2021 Mar 17;22(6):3076.
  12. Madlala T, Okpeku M, Adeleke MA. Understanding the interactions between Eimeria infection and gut microbiota, towards the control of chicken coccidiosis: a review. Parasite. 2021 Jun 2;28:48.
  13. Knecht D, Cholewińska P, Jankowska-Mąkosa A, Czyż K. Development of swine’s digestive tract microbiota and its relation to production indices—A review. Animals. 2020 Mar 21;10(3):527.
  14. Infusino F, Marazzato M, Mancone M, Fedele F, Mastroianni CM, Severino P, Ceccarelli G, Santinelli L, Cavarretta E, Marullo AG, Miraldi F. Diet supplementation, probiotics, and nutraceuticals in SARS-CoV-2 infection: a scoping review. Nutrients. 2020 Jun 8;12(6):1718.
  15. Shehata AM, Paswan VK, Attia YA, Abdel-Moneim AM, Abougabal MS, Sharaf M, Elmazoudy R, Alghafari WT, Osman MA, Farag MR, Alagawany M. Managing gut microbiota through in ovo nutrition influences early-life programming in broiler chickens. Animals. 2021 Dec 7;11(12):3491.
  16. Shehata AA, Yalçın S, Latorre JD, Basiouni S, Attia YA, Abd El-Wahab A, Visscher C, El-Seedi HR, Huber C, Hafez HM, Eisenreich W. Probiotics, prebiotics, and phytogenic substances for optimizing gut health in poultry. Microorganisms. 2022 Feb 8;10(2):395.
  17. Mahmud MR, Tamanna SK, Akter S, Mazumder L, Akter S, Hasan MR, Acharjee M, Esti IZ, Islam MS, Shihab MM, Nahian M. Role of bacteriophages in shaping gut microbial community. Gut Microbes. 2024 Dec 31;16(1):2390720.
  18. Barathan M, Ng SL, Lokanathan Y, Ng MH, Law JX. The profound influence of gut microbiome and extracellular vesicles on animal health and disease. International journal of molecular sciences. 2024 Apr 4;25(7):4024.
  19. Guo F, Geng Y, Abbas W, Zhen W, Wang S, Huang Y, Guo Y, Ma Q, Wang Z. Vitamin D3 nutritional status affects gut health of Salmonella-challenged laying hens. Frontiers in Nutrition. 2022 May 10;9:888580.
  20. Pandupuspitasari NS, Sugiharto S, Khan FA, Raza MA, Lestari DA, Setiaji A, Agusetyaningsih I. Gut microbiota profile, potential engineering techniques and its genetic and epigenetic implications in poultry health. World Journal of Microbiology and Biotechnology. 2025 Dec;41(12):488.
  21. Aruwa CE, Pillay C, Nyaga MM, Sabiu S. Poultry gut health–microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies. Journal of Animal Science and Biotechnology. 2021 Dec 2;12(1):119.
  22. Welch CB, Ryman VE, Pringle TD, Lourenco JM. Utilizing the Gastrointestinal Microbiota to Modulate Cattle Health through the Microbiome-Gut-Organ Axes. Microorganisms 2022, 10, 1391.
  23. Engel P, Moran NA. The gut microbiota of insects–diversity in structure and function. FEMS microbiology reviews. 2013 Sep 1;37(5):699-735.
  24. Turner M, Van Hulzen L, Guse K, Agany D, Pietri JE. The gut microbiota confers resistance against Salmonella Typhimurium in cockroaches by modulating innate immunity. IScience. 2024 Dec 20;27(12).
  25. Bertorello S, Cei F, Fink D, Niccolai E, Amedei A. The future exploring of gut microbiome-immunity interactions: From in vivo/vitro models to in silico innovations. Microorganisms. 2024 Sep 4;12(9):1828.
  26. Kumar D, Shepherd FK, Springer NL, Mwangi W, Marthaler DG. Rotavirus infection in swine: genotypic diversity, immune responses, and role of gut microbiome in rotavirus immunity. Pathogens. 2022 Sep 22;11(10):1078.
  27. Saint-Martin V, Quéré P, Trapp S, Guabiraba R. Uncovering the core principles of the gut-lung axis to enhance innate immunity in the chicken. Frontiers in Immunology. 2022 Oct 4;13:956670.
  28. Almire F, Terhzaz S, Terry S, McFarlane M, Gestuveo RJ, Szemiel AM, Varjak M, McDonald A, Kohl A, Pondeville E. Sugar feeding protects against arboviral infection by enhancing gut immunity in the mosquito vector Aedes aegypti. PLoS pathogens. 2021 Sep 2;17(9):e1009870.
  29. Vieira SM, Pagovich OE, Kriegel M. Diet, microbiota and autoimmune diseases. Lupus. 2014 May;23(6):518-26.
  30. Rio-Aige K, Selma-Royo M, Cabrera-Rubio R, González S, Martínez-Costa C, Castell M, Rodríguez-Lagunas MJ, Collado MC, Pérez-Cano FJ. Maternal diet shapes infant microbiota and defensive capacity against infections in early life via differential human milk composition. EBioMedicine. 2025 Aug 1;118.
  31. Vanalli C, Falvo C, Crowley D, Schwarz B, Plowright R, Hudson PJ, Rynda-Apple A, Cattadori IM. Modeling the dietary effects on bat viral shedding and potential consequences for pathogen spillover. bioRxiv. 2024 Jun 23:2024-06.
  32. Myhill LJ, Williams AR. Diet‐microbiota crosstalk and immunity to helminth infection. Parasite Immunology. 2023 Apr;45(4):e12965.
  33. Julio-Pieper M, López-Aguilera A, Eyzaguirre-Velásquez J, Olavarría-Ramírez L, Ibacache-Quiroga C, Bravo JA, Cruz G. Gut susceptibility to viral invasion: contributing roles of diet, microbiota and enteric nervous system to mucosal barrier preservation. International journal of molecular sciences. 2021 Apr 29;22(9):4734.
  34. Guo Y, Zhu X, Zeng M, Qi L, Tang X, Wang D, Zhang M, Xie Y, Li H, Yang X, Chen D. A diet high in sugar and fat influences neurotransmitter metabolism and then affects brain function by altering the gut microbiota. Translational psychiatry. 2021 May 27;11(1):328.
  35. Larroya A, Pantoja J, Codoñer-Franch P, Cenit MC. Towards tailored gut microbiome-based and dietary interventions for promoting the development and maintenance of a healthy brain. Frontiers in pediatrics. 2021 Jul 1;9:705859.
  36. Rapozo DC, Bernardazzi C, de Souza HS. Diet and microbiota in inflammatory bowel disease: The gut in disharmony. World journal of gastroenterology. 2017 Mar 28;23(12):2124.
  37. Caio G, Lungaro L, Segata N, Guarino M, Zoli G, Volta U, De Giorgio R. Effect of gluten-free diet on gut microbiota composition in patients with celiac disease and non-celiac gluten/wheat sensitivity. Nutrients. 2020 Jun 19;12(6):1832.
  38. Negash A. Gut microbiota ecology role in animal nutrition and health performance. J. Clin. Microbiol. Antimicrob. 2022;6(001).
  39. O’Doherty J, Dowley A, Conway E, Sweeney T. Nutritional strategies to mitigate post-weaning challenges in pigs: A focus on glucans, vitamin D, and selenium. Animals. 2023 Dec 19;14(1):13.
  40. Yan J, Kim CH, Chesser L, Ramirez JL, Stone CM. Nutritional stress compromises mosquito fitness and antiviral immunity, while enhancing dengue virus infection susceptibility. Communications biology. 2023 Nov 6;6(1):1123.
  41. Mafra D, Borges NA, Baptista BG, Martins LF, Borland G, Shiels PG, Stenvinkel P. What can the gut microbiota of animals teach us about the relationship between nutrition and burden of lifestyle diseases?. Nutrients. 2024 Jun 6;16(11):1789.
  42. Lv Y, Zhou Y, Lu H, Dong H, He Z. Determinants of piglet gut microbiome colonization: roles of genetics, nutrition, therapeutics, and the impact of enteric pathogens like PEDV. Frontiers in Cellular and Infection Microbiology. 2025 Aug 25;15:1626239.
  43. Mehta S, Huey SL, McDonald D, Knight R, Finkelstein JL. Nutritional interventions and the gut microbiome in children. Annual Review of Nutrition. 2021 Oct 11;41(1):479-510.
  44. Humphries DL, Scott ME, Vermund SH, editors. Nutrition and infectious diseases. Cham, Switzerland: Springer International Publishing; 2021.
  45. Alam S, Bhuiyan FR, Emon TH, Hasan M. Prospects of nutritional interventions in the care of COVID-19 patients. Heliyon. 2021 Feb 1;7(2).
  46. Leonardi R, Lo Bianco M, Spinello S, Betta P, Gagliano C, Calabrese V, Polizzi A, Malaguarnera G. Resveratrol as an Adjunct Antiviral Agent in Pediatric Viral Infections: A Review on Mechanistic Insights and Gut Microbiota Modulation. International Journal of Molecular Sciences. 2025 Nov 24;26(23):11341.
  47. Mills S, Stanton C, Lane JA, Smith GJ, Ross RP. Precision nutrition and the microbiome, part I: current state of the science. Nutrients. 2019 Apr 24;11(4):923.
  48. Abeltino A, Hatem D, Serantoni C, Riente A, De Giulio MM, De Spirito M, De Maio F, Maulucci G. Unraveling the gut microbiota: implications for precision nutrition and personalized medicine. Nutrients. 2024 Nov 6;16(22):3806.
  49. Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LM. The interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies. Nutrients. 2021 Mar;13(3):886.
  50. Honce R, Schultz-Cherry S. They are what you eat: shaping of viral populations through nutrition and consequences for virulence. PLoS pathogens. 2020 Aug 13;16(8):e1008711.
  51. Cassotta M, Forbes-Hernández TY, Calderón Iglesias R, Ruiz R, Elexpuru Zabaleta M, Giampieri F, Battino M. Links between nutrition, infectious diseases, and microbiota: Emerging technologies and opportunities for human-focused research. Nutrients. 2020 Jun 19;12(6):1827.
  52. Vermund SH, Scott ME, Humphries DL. Public health and clinical implications of nutrition-infection interactions. InNutrition and Infectious Diseases: Shifting the Clinical Paradigm 2020 Dec 11 (pp. 459-481). Cham: Springer International Publishing.
  53. Leulier F, MacNeil LT, Lee WJ, Rawls JF, Cani PD, Schwarzer M, Zhao L, Simpson SJ. Integrative physiology: at the crossroads of nutrition, microbiota, animal physiology, and human health. Cell metabolism. 2017 Mar 7;25(3):522-34.
  54. Gavkare AM, Nanaware NL, Sonar MN, Dhotre SV, Mumbre SS, Nagoba BS. Gut microbiome and viral infections: A hidden nexus for immune protection. World Journal of Virology. 2025 Sep 25;14(3):111912.
  55. Borrego-Ruiz A, Borrego JJ. The Gut Microbiome in Enteric Viral Infections: Underlying Mechanisms and Therapeutic Approaches. Microorganisms. 2025 Sep 25;13(10):2247.
  56. Altomare A, Giovanetti M, Baldaro F, Ciccozzi M, Cicala M, Guarino MP. The prevention of viral infections: the role of intestinal microbiota and nutritional factors. Nutrients. 2024 Jul 27;16(15):2445.
  57. Tsui Y, Wu X, Zhang X, Peng Y, Mok CK, Chan FK, Ng SC, Tun HM. Short-chain fatty acids in viral infection: the underlying mechanisms, opportunities, and challenges. Trends in microbiology. 2025 Mar 1;33(3):302-20.
  58. Deng Y, Yang S, Zhang L, Chen C, Cheng X, Hou C. Chronic bee paralysis virus exploits host antimicrobial peptides and alters gut microbiota composition to facilitate viral infection. The ISME Journal. 2024 Jan 1;18(1):wrae051.
  59. Avitabile E, Menotti L, Croatti V, Giordani B, Parolin C, Vitali B. Protective mechanisms of vaginal lactobacilli against sexually transmitted viral infections. International Journal of Molecular Sciences. 2024 Aug 23;25(17):9168.
  60. Jones DN, Ravelomanantsoa NA, Yeoman CJ, Plowright RK, Brook CE. Do gastrointestinal microbiomes play a role in bats’ unique viral hosting capacity?. Trends in microbiology. 2022 Jul 1;30(7):632-42.
  61. Harper A, Vijayakumar V, Ouwehand AC, Ter Haar J, Obis D, Espadaler J, Binda S, Desiraju S, Day R. Viral infections, the microbiome, and probiotics. Frontiers in Cellular and Infection Microbiology. 2021 Feb 12;10:596166.
  62. Shelly A, Gupta P, Ahuja R, Srichandan S, Meena J, Majumdar T. Impact of microbiota: a paradigm for evolving herd immunity against viral diseases. Viruses. 2020 Oct 10;12(10):1150.
  63. Shahbazi R, Yasavoli-Sharahi H, Alsadi N, Ismail N, Matar C. Probiotics in treatment of viral respiratory infections and neuroinflammatory disorders. Molecules. 2020 Oct 22;25(21):4891.
  64. Chelakkot C, Ghim J, Ryu SH. Mechanisms regulating intestinal barrier integrity and its pathological implications. Experimental & molecular medicine. 2018 Aug;50(8):1-9.
  65. Zhang Y, Si L, Shu X, Qiu C, Wan X, Li H, Ma S, Jin X, Wei Z, Hu H. Gut microbiota contributes to protection against porcine deltacoronavirus infection in piglets by modulating intestinal barrier and microbiome. Microbiome. 2025 Apr 7;13(1):93.
  66. Zhang F, Lau RI, Liu Q, Su Q, Chan FK, Ng SC. Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications. Nature reviews Gastroenterology & hepatology. 2023 May;20(5):323-37.
  67. Li L, Sun X, Zhao D, Dai H. Pharmacological applications and action mechanisms of phytochemicals as alternatives to antibiotics in pig production. Frontiers in Immunology. 2021 Dec 9;12:798553.
  68. Lerner A, Neidhöfer S, Matthias T. The gut microbiome feelings of the brain: a perspective for non-microbiologists. Microorganisms. 2017 Oct 12;5(4):66.
  69. Forcina G, Pérez-Pardal L, Carvalheira J, Beja-Pereira A. Gut microbiome studies in livestock: achievements, challenges, and perspectives. Animals. 2022 Nov 30;12(23):3375.
Regular Issue Subscription Review Article
Volume 03
Issue 01
Received 03/02/2026
Accepted 05/02/2026
Published 20/02/2026
Publication Time 17 Days
123

Login


My IP

PlumX Metrics