AccScience Publishing / MI / Online First / DOI: 10.36922/MI025340084
REVIEW ARTICLE

Developmental symbiosis in immunity: Microbiome–immune interactions from infancy to adulthood

Ángel R. Rábago-Monzón1 David A. Armienta-Rojas1 Alberto K. De la Herrán-Arita1*
Show Less
1 Department of neuroscience, School of Medicine, Autonomous University of Sinaloa, Culiacán, Sinaloa, México
Received: 21 August 2025 | Revised: 16 December 2025 | Accepted: 21 January 2026 | Published online: 24 April 2026
© 2026 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

The maturation of the immune system is not an isolated, genetically pre-programmed process but rather the outcome of a deeply integrated partnership between host and microbial communities, a phenomenon we term developmental symbiosis. This review synthesizes evidence from evolutionary biology, ecology, and immunology to describe how symbiotic relationships shape immune trajectories across the human lifespan. We begin by addressing the co-evolutionary foundations of this partnership, illustrating how ancient microbial encounters drove the selection of key molecular components, including pathogen-associated molecular pattern recognition by Toll-like receptors (TLRs) and the viral origins of recombination-activating genes. Moving away from a siloed structure, we examine the lifespan chronologically, integrating mechanistic insights with clinical pathology for each developmental window. We detail the unique immune behaviors of the prenatal period, specifically the window of heightened tolerance, followed by the critical priming events of neonatal colonization, the expansive education of infancy, the hormonal modulations of adolescence, and the dysbiotic shifts of aging. Within each stage, we highlight how environmental disruptions, such as antibiotic use or delivery mode changes, can permanently recalibrate immune set-points. Finally, we evaluate the current status of therapeutic modulations, including probiotics and fecal microbiota transplantation, emphasizing the need for precision interventions that are tailored in accordance to the temporal specificity of immune development.

Keywords
Microbiota–immune interactions
Developmental immunology
Symbiosis
Dysbiosis
Funding
None.
Conflict of interest
The authors declare that they have no conflicts of interest.
References
  1. Donald K, Finlay BB. Early-life interactions between the microbiota and immune system: impact on immune system development and atopic disease. Nat Rev Immunol. 2023;23(11):735-748. doi: 10.1038/s41577-023-00874-w
  2. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121-141. doi: 10.1016/j.cell.2014.03.011
  3. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336(6086):1268-1273. doi: 10.1126/science.1223490
  4. Gordon HA, Pesti L. The gnotobiotic animal as a tool in the study of host microbial relationships. Bacteriol Rev. 1971;35(4):390-429. doi: 10.1128/br.35.4.390-429.1971
  5. Tissier H. Recherches sur la flore intestinale des nourrissons (état normal et pathologique) [Research on the intestinal flora of infants (normal and pathological state)]. Paris: G. Carré et C. Naud. 1900. [in French]
  6. Rook GAW. 99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: darwinian medicine and the ‘hygiene’ or ‘old friends’ hypothesis. Clin Exp Immunol. 2010;160(1):70-79. doi: 10.1111/j.1365-2249.2010.04133.x
  7. Strachan DP. Hay fever, hygiene, and household size. BMJ. 1989;299(6710):1259-1260. doi: 10.1136/bmj.299.6710.1259
  8. Poltorak A, He X, Smirnova I, et al. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science. 1998;282(5396):2085-2088. doi: 10.1126/science.282.5396.2085
  9. Agrawal A, Eastman QM, Schatz DG. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature. 1998;394(6695):744-751. doi: 10.1038/29457
  10. Lee YK, Mazmanian SK. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science. 2010;330(6012):1768-1773. doi: 10.1126/science.1195568
  11. Koren O, Goodrich JK, Cullender TC, et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012;150(3):470-480. doi: 10.1016/j.cell.2012.07.008
  12. Gomez de Agüero M, Ganal-Vonarburg SC, Fuhrer T, et al. The maternal microbiota drives early postnatal innate immune development. Science. 2016;351(6279):1296-1302. doi: 10.1126/science.aad2571
  13. Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971-11975. doi: 10.1073/pnas.1002601107
  14. Huurre A, Kalliomäki M, Rautava S, Rinne M, Salminen S, Isolauri E. Mode of delivery - effects on gut microbiota and humoral immunity. Neonatology. 2008;93(4):236-240. doi: 10.1159/000111102
  15. Bäckhed F, Roswall J, Peng Y, et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015;17(5):690-703. doi: 10.1016/j.chom.2015.04.004
  16. Hinzke T, Kleiner M, Breusing C, et al. Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis. mBio. 2019;10(6):e02243-19. doi: 10.1128/mBio.02243-19
  17. Srivastava R, Eswar K, Ramesh SSR, et al. Zebrafish as a versatile model organism: From tanks to treatment. MedComm–Future Med. 2025;4(3). doi: 10.1002/mef2.70028.
  18. Olszak T, An D, Zeissig S, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336(6080):489-493. doi: 10.1126/science.1219328
  19. Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016;352(6285):539-544. doi: 10.1126/science.aad9378
  20. Zicari AM, Mora B, Lollobrigida V, et al. Immunogenetic investigation in vernal keratoconjunctivitis. Pediatr Allergy Immunol. 2014;25(5):508-510. doi: 10.1111/pai.12231
  21. Randall TD, Mebius RE. The development and function of mucosal lymphoid tissues: a balancing act with micro-organisms. Mucosal Immunol. 2014;7(3):455-466. doi: 10.1038/mi.2014.11
  22. Sudo N, Sawamura S, Tanaka K, Aiba Y, Kubo C, Koga Y. The requirement of intestinal bacterial flora for the development of an IgE production system fully susceptible to oral tolerance induction. J Immunol. 1997;159(4):1739- 1745.
  23. Atarashi K, Tanoue T, Shima T, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011;331(6015):337-341. doi: 10.1126/science.1198469
  24. Round JL, Lee SM, Li J, et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science. 2011;332(6032):974-977. doi: 10.1126/science.1206095
  25. Ivanov II, Atarashi K, Manel N, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139(3):485-498. doi: 10.1016/j.cell.2009.09.033
  26. Gaboriau-Routhiau V, Rakotobe S, Lécuyer E, et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity. 2009;31(4):677-689. doi: 10.1016/j.immuni.2009.08.020
  27. de Koff EM, van Baarle D, van Houten MA, et al. Mode of delivery modulates the intestinal microbiota and impacts the response to vaccination. Nat Commun. 2022;13(1):6638. doi: 10.1038/s41467-022-34155-2
  28. Li D, Cheng J, Zhu Z, et al. Treg-inducing capacity of genomic DNA of Bifidobacterium longum subsp. infantis. Allergy Asthma Proc. 2020;41(5):372-385. doi: 10.2500/aap.2020.41.200064
  29. Arrieta MC, Stiemsma LT, Dimitriu PA, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015;7(307):307ra152. doi: 10.1126/scitranslmed.aab2271
  30. Markle JG, Frank DN, Mortin-Toth S, et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013;339(6123):1084-1088. doi: 10.1126/science.1233521
  31. Jiminez JA, Uwiera TC, Douglas Inglis G, Uwiera RR. Animal models to study acute and chronic intestinal inflammation in mammals. Gut Pathog. 2015;7:29. doi: 10.1186/s13099-015-0076-y
  32. Camacho-Zamora A, Rábago-Monzón AR, Armienta- Rojas DA, et al. The gut–brain axis: Collective impact of psychosomatic conditions and gut microbiota on health and disease. J Clin Basic Psychosom. 2025;3(3):25–44. doi: 10.36922/JCBP025040008
  33. Lathrop SK, Bloom SM, Rao SM, et al. Peripheral education of the immune system by colonic commensal microbiota. Nature. 2011;478(7368):250–254. doi: 10.1038/nature10434
  34. Franceschi C, Bonafè M, Valensin S, et al. Inflamm-aging. An evolutionary perspective on immunosenescence. Ann NY Acad Sci. 2000;908(1):244-254. doi: 10.1111/j.1749-6632.2000.tb06651.x
  35. O’Toole PW, Jeffery IB. Gut microbiota and aging. Science. 2015;350(6265):1214-1215. doi: 10.1126/science.aac8469
  36. Thevaranjan N, Puchta A, Schulz C, et al. Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction. Cell Host Microbe. 2017;21(4):455-466.e4. doi: 10.1016/j.chom.2017.03.002
  37. Belkaid Y, Harrison OJ. Homeostatic Immunity and the Microbiota. Immunity. 2017;46(4):562-576. doi: 10.1016/j.immuni.2017.04.008
  38. Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature. 2016;535(7610):75-84. doi: 10.1038/nature18848
  39. Kinnebrew MA, Pamer EG. Innate immune signaling in defense against intestinal microbes. Immunol Rev. 2012;245(1):113-131. doi: 10.1111/j.1600-065X.2011.01081.x
  40. Sefik E, Geva-Zatorsky N, Oh S, et al. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. Science. 2015;349(6251):993-997. doi: 10.1126/science.aaa9420
  41. Lee YK, Menezes JS, Umesaki Y, Mazmanian SK. Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci USA. 2011;108(Suppl 1):4615-4622. doi: 10.1073/pnas.1000082107
  42. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122(1):107-118. doi: 10.1016/j.cell.2005.05.007
  43. Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci USA. 2010;107(27):12204-12209. doi: 10.1073/pnas.0909122107
  44. Alemán-Villa KM, Armienta-Rojas DA, Camberos- Barraza J, et al. Neuroinflammation across the Spectrum of Neurodegenerative Diseases: Mechanisms and Therapeutic Frontiers. Neuroimmunomodulation. 2025;32(1):278-305. doi: 10.1159/000548021
  45. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell. 2004;118(2):229-241. doi: 10.1016/j.cell.2004.07.002
  46. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9(5):313-323. doi: 10.1038/nri2515
  47. Kalliomäki M, Salminen S, Arvilommi H, Kero P, Koskinen P, Isolauri E. Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. Lancet. 2001;357(9262):1076-1079. doi: 10.1016/S0140-6736(00)04259-8
  48. Kalliomäki M, Salminen S, Poussa T, Arvilommi H, Isolauri E. Probiotics and prevention of atopic disease: 4-year follow-up of a randomised placebo-controlled trial. Lancet. 2003;361(9372):1869-1871. doi: 10.1016/S0140-6736(03)13490-3
  49. Kalliomäki M, Salminen S, Poussa T, Isolauri E. Probiotics during the first 7 years of life: a cumulative risk reduction of eczema in a randomized, placebo-controlled trial. J Allergy Clin Immunol. 2007;119(4):1019-1021. doi: 10.1016/j.jaci.2006.12.608
  50. Asghari KM, Dolatkhah N, Ayromlou H, Mirnasiri F, Dadfar T, Hashemian M. The effect of probiotic supplementation on the clinical and para-clinical findings of multiple sclerosis: a randomized clinical trial. Sci Rep. 2023;13(1):18577. doi: 10.1038/s41598-023-46047-6
  51. Hill C, Guarner F, Reid G, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;11(8):506-514. doi: 10.1038/nrgastro.2014.66
  52. Camberos-Barraza J, Guadrón-Llanos AM, De la Herrán- Arita AK. The Gut Microbiome-Neuroglia Axis: Implications for Brain Health, Inflammation, and Disease. Neuroglia. 2024;5(3):254-273. doi: 10.3390/neuroglia5030018
  53. Gibson GR, Hutkins R, Sanders ME, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491-502. doi: 10.1038/nrgastro.2017.75
  54. Hsiao EY, McBride SW, Hsien S, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;155(7):1451- 1463. doi: 10.1016/j.cell.2013.11.024
  55. Sampson TR, Debelius JW, Thron T, et al. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease. Cell. 2016;167(6):1469-1480.e12. doi: 10.1016/j.cell.2016.11.018
  56. van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407-415. doi: 10.1056/NEJMoa1205037
  57. Kang DW, Adams JB, Gregory AC, et al. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017;5(1):10.doi: 10.1186/s40168-016-0225-7
  58. Routy B, Le Chatelier E, Derosa L, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science. 2018;359(6371):91-97. doi: 10.1126/science.aan3706
  59. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027-1031. doi: 10.1038/nature05414
  60. Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341(6150):1241214. doi: 10.1126/science.1241214
  61. Keane L, Clarke G, Cryan JF. A role for microglia in mediating the microbiota-gut-brain axis. Nat Rev Immunol. 2025;25(11):847-861. doi: 10.1038/s41577-025-01188-9

62. Loh JS, Mak WQ, Tan LKS, et al. Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases. Signal Transduct Target Ther. 2024;9(1):37. doi: 10.1038/s41392-024-01743-1

Share
Back to top
Microbes & Immunity, Electronic ISSN: 3029-2883 Print ISSN: 3041-0886, Published by AccScience Publishing