Skip to main content

Advertisement

Log in

The impact of the gut microbiota on T cell ontogeny in the thymus

  • Review
  • Published:
Cellular and Molecular Life Sciences Aims and scope Submit manuscript

Abstract

The intestinal microbiota is critical for the development of gut-associated lymphoid tissues, including Peyer’s patches and mesenteric lymph nodes, and is instrumental in educating the local as well as systemic immune system. In addition, it also impacts the development and function of peripheral organs, such as liver, lung, and the brain, in health and disease. However, whether and how the intestinal microbiota has an impact on T cell ontogeny in the hymus remains largely unclear. Recently, the impact of molecules and metabolites derived from the intestinal microbiota on T cell ontogeny in the thymus has been investigated in more detail. In this review, we will discuss the recent findings in the emerging field of the gut-thymus axis and we will highlight the current questions and challenges in the field.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

Data availability

Not applicable.

References

  1. Blumberg R, Powrie F (2012) Microbiota, disease, and back to health: a metastable journey. Sci Transl Med 4(137):13rv77

    Article  CAS  Google Scholar 

  2. Belkaid Y, Hand TW (2014) Role of the microbiota in immunity and inflammation. Cell 157(1):121–141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Deshmukh HS et al (2014) The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice. Nat Med 20(5):524–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Li F et al (2017) The microbiota maintain homeostasis of liver-resident gammadeltaT-17 cells in a lipid antigen/CD1d-dependent manner. Nat Commun 7:13839

    Article  PubMed  CAS  Google Scholar 

  5. Gonzalez-Perez G et al (2016) Maternal antibiotic treatment impacts development of the neonatal intestinal microbiome and antiviral immunity. J Immunol 196(9):3768–3779

    Article  CAS  PubMed  Google Scholar 

  6. Geuking MB, Burkhard R (2020) Microbial modulation of intestinal T helper cell responses and implications for disease and therapy. Mucosal Immunol 13(6):855–866

    Article  CAS  PubMed  Google Scholar 

  7. Strachan DP (1989) Hay fever, hygiene, and household size. BMJ 299(6710):1259–1260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bach JF (2002) The effect of infections on susceptibility to autoimmune and allergic diseases. N Engl J Med 347(12):911–920

    Article  PubMed  Google Scholar 

  9. Azad MB et al (2013) Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity. Allergy Asthma Clin Immunol 9(1):15

    Article  PubMed  PubMed Central  Google Scholar 

  10. Deckers J et al (2021) Protection against allergies: microbes, immunity, and the farming effect. Eur J Immunol 51(10):2387–2398

    Article  CAS  PubMed  Google Scholar 

  11. Riedler J et al (2001) Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey. Lancet 358(9288):1129–1133

    Article  CAS  PubMed  Google Scholar 

  12. Braun-Fahrlander C et al (2002) Environmental exposure to endotoxin and its relation to asthma in school-age children. N Engl J Med 347(12):869–877

    Article  PubMed  Google Scholar 

  13. Cahenzli J et al (2013) Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe 14(5):559–570

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. McCoy KD et al (2006) Natural IgE production in the absence of MHC Class II cognate help. Immunity 24(3):329–339

    Article  CAS  PubMed  Google Scholar 

  15. Stinson LF et al (2019) The not-so-sterile womb: evidence that the human fetus is exposed to bacteria prior to birth. Front Microbiol 10:1124

    Article  PubMed  PubMed Central  Google Scholar 

  16. Milani C et al (2017) The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev 81(4)

  17. Romano-Keeler J, Weitkamp JH (2015) Maternal influences on fetal microbial colonization and immune development. Pediatr Res 77(1–2):189–195

    Article  PubMed  Google Scholar 

  18. Nuriel-Ohayon M et al (2016) Microbial changes during pregnancy, birth, and infancy. Front Microbiol 7:1031

    Article  PubMed  PubMed Central  Google Scholar 

  19. Gomez de Aguero M et al (2016) The maternal microbiota drives early postnatal innate immune development. Science 351(6279):1296–1302

    Article  PubMed  CAS  Google Scholar 

  20. Thorburn AN et al (2015) Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun 6:7320

    Article  CAS  PubMed  Google Scholar 

  21. Furusawa Y et al (2013) Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504(7480):446–450

    Article  CAS  PubMed  Google Scholar 

  22. Stiemsma LT, Turvey SE (2017) Asthma and the microbiome: defining the critical window in early life. Allergy Asthma Clin Immunol 13:3

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Ichinohe T et al (2011) Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci USA 108(13):5354–5359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Perry RJ et al (2016) Acetate mediates a microbiome-brain-beta-cell axis to promote metabolic syndrome. Nature 534(7606):213–217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Buffington SA et al (2016) Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring. Cell 165(7):1762–1775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Clarke TB et al (2010) Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat Med 16(2):228–231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Rooks MG, Garrett WS (2016) Gut microbiota, metabolites and host immunity. Nat Rev Immunol 16(6):341–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Abt MC et al (2012) Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 37(1):158–170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ennamorati M et al (2020) Intestinal microbes influence development of thymic lymphocytes in early life. Proc Natl Acad Sci USA 117(5):2570–2578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Ikuta K et al (1990) A developmental switch in thymic lymphocyte maturation potential occurs at the level of hematopoietic stem cells. Cell 62(5):863–874

    Article  CAS  PubMed  Google Scholar 

  31. Havran WL, Allison JP (1988) Developmentally ordered appearance of thymocytes expressing different T-cell antigen receptors. Nature 335(6189):443–445

    Article  CAS  PubMed  Google Scholar 

  32. den Braber I et al (2012) Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans. Immunity 36(2):288–297

    Article  CAS  Google Scholar 

  33. Hartvigsson O et al (2021) Associations of maternal and infant metabolomes with immune maturation and allergy development at 12 months in the Swedish NICE-cohort. Sci Rep 11(1):12706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Yang L et al (2020) T cell tolerance in early life. Front Immunol 11:576261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Prelog M et al (2009) Thymectomy in early childhood: significant alterations of the CD4(+)CD45RA(+)CD62L(+) T cell compartment in later life. Clin Immunol 130(2):123–132

    Article  CAS  PubMed  Google Scholar 

  36. Dzhagalov I, Phee H (2012) How to find your way through the thymus: a practical guide for aspiring T cells. Cell Mol Life Sci 69(5):663–682

    Article  CAS  PubMed  Google Scholar 

  37. Aghaallaei N, Bajoghli B (2018) Making thymus visible: understanding T-cell development from a new perspective. Front Immunol 9:375

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Petrie HT, Zuniga-Pflucker JC (2007) Zoned out: functional mapping of stromal signaling microenvironments in the thymus. Annu Rev Immunol 25:649–679

    Article  CAS  PubMed  Google Scholar 

  39. Koch U, Radtke F (2011) Mechanisms of T cell development and transformation. Annu Rev Cell Dev Biol 27:539–562

    Article  CAS  PubMed  Google Scholar 

  40. Yu W et al (2015) Clonal deletion prunes but does not eliminate self-specific alphabeta CD8(+) T lymphocytes. Immunity 42(5):929–941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Perry JSA et al (2014) Distinct contributions of Aire and antigen-presenting-cell subsets to the generation of self-tolerance in the thymus. Immunity 41(3):414–426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Savage PA et al (2020) Regulatory T cell development. Annu Rev Immunol 38:421–453

    Article  CAS  PubMed  Google Scholar 

  43. Kim JM et al (2007) Regulatory T cells prevent catastrophic autoimmunity throughout the lifespan of mice. Nat Immunol 8(2):191–197

    Article  CAS  PubMed  Google Scholar 

  44. Sakaguchi S et al (1995) Immunologic self-tolerance maintained by activated T cells expressing IL-2 receptor alpha-chains (CD25). Breakdown of a single mechanism of self-tolerance causes various autoimmune diseases. J Immunol 155(3):1151–1164

    CAS  PubMed  Google Scholar 

  45. Fontenot JD et al (2003) Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat Immunol 4(4):330–336

    Article  CAS  PubMed  Google Scholar 

  46. Hori S et al (2003) Control of regulatory T cell development by the transcription factor Foxp3. Science 299(5609):1057–1061

    Article  CAS  PubMed  Google Scholar 

  47. Thornton AM et al (2010) Expression of Helios, an Ikaros transcription factor family member, differentiates thymic-derived from peripherally induced Foxp3+ T regulatory cells. J Immunol 184(7):3433–3441

    Article  CAS  PubMed  Google Scholar 

  48. Lio CW, Hsieh CS (2008) A two-step process for thymic regulatory T cell development. Immunity 28(1):100–111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Tai X et al (2013) Foxp3 transcription factor is proapoptotic and lethal to developing regulatory T cells unless counterbalanced by cytokine survival signals. Immunity 38(6):1116–1128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Chiba A et al (2018) Mucosal-associated invariant T cells in autoimmune diseases. Front Immunol 9:1333

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. Van Kaer L, Wu L (2018) Therapeutic potential of invariant natural killer T cells in autoimmunity. Front Immunol 9:519

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Shiromizu CM, Jancic CC (2018) gammadelta T lymphocytes: an effector cell in autoimmunity and infection. Front Immunol 9:2389

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Seach N et al (2013) Double-positive thymocytes select mucosal-associated invariant T cells. J Immunol 191(12):6002–6009

    Article  CAS  PubMed  Google Scholar 

  54. Gold MC et al (2013) Human thymic MR1-restricted MAIT cells are innate pathogen-reactive effectors that adapt following thymic egress. Mucosal Immunol 6(1):35–44

    Article  CAS  PubMed  Google Scholar 

  55. Hu Z et al (2019) NKT cells in mice originate from cytoplasmic CD3-positive, CD4(-)CD8(-) double-negative thymocytes that express CD44 and IL-7Ralpha. Sci Rep 9(1):1874

  56. Treiner E et al (2003) Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1. Nature 422(6928):164–169

    Article  CAS  PubMed  Google Scholar 

  57. Franciszkiewicz K et al (2016) MHC class I-related molecule, MR1, and mucosal-associated invariant T cells. Immunol Rev 272(1):120–138

    Article  CAS  PubMed  Google Scholar 

  58. Magalhaes I et al (2015) Mucosal-associated invariant T cell alterations in obese and type 2 diabetic patients. J Clin Invest 125(4):1752–1762

    Article  PubMed  PubMed Central  Google Scholar 

  59. Rouxel O et al (2017) Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes. Nat Immunol 18(12):1321–1331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Koay HF et al (2016) A three-stage intrathymic development pathway for the mucosal-associated invariant T cell lineage. Nat Immunol 17(11):1300–1311

    Article  CAS  PubMed  Google Scholar 

  61. Salou M et al (2019) A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets. J Exp Med 216(1):133–151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Lu Y et al (2019) SLAM receptors foster iNKT cell development by reducing TCR signal strength after positive selection. Nat Immunol 20(4):447–457

    Article  CAS  PubMed  Google Scholar 

  63. Griewank K et al (2007) Homotypic interactions mediated by Slamf1 and Slamf6 receptors control NKT cell lineage development. Immunity 27(5):751–762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Legoux F et al (2019) Molecular mechanisms of lineage decisions in metabolite-specific T cells. Nat Immunol 20(9):1244–1255

    Article  CAS  PubMed  Google Scholar 

  65. Bendelac A et al (2007) The biology of NKT cells. Annu Rev Immunol 25:297–336

    Article  CAS  PubMed  Google Scholar 

  66. Godfrey DI et al (2010) Raising the NKT cell family. Nat Immunol 11(3):197–206

    Article  CAS  PubMed  Google Scholar 

  67. Hammond K et al (1998) Three day neonatal thymectomy selectively depletes NK1.1+ T cells. Int Immunol 10(10):1491–1499

    Article  CAS  PubMed  Google Scholar 

  68. Pellicci DG et al (2002) A natural killer T (NKT) cell developmental pathway involving a thymus-dependent NK1.1(−)CD4(+) CD1d-dependent precursor stage. J Exp Med 195(7):835–844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Bendelac A (1995) Positive selection of mouse NK1+ T cells by CD1-expressing cortical thymocytes. J Exp Med 182(6):2091–2096

    Article  CAS  PubMed  Google Scholar 

  70. Kawano T et al (1997) CD1d-restricted and TCR-mediated activation of valpha14 NKT cells by glycosylceramides. Science 278(5343):1626–1629

    Article  CAS  PubMed  Google Scholar 

  71. Benlagha K et al (2002) A thymic precursor to the NK T cell lineage. Science 296(5567):553–555

    Article  CAS  PubMed  Google Scholar 

  72. Lazarevic V et al (2009) The gene encoding early growth response 2, a target of the transcription factor NFAT, is required for the development and maturation of natural killer T cells. Nat Immunol 10(3):306–313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Kovalovsky D et al (2008) The BTB-zinc finger transcriptional regulator PLZF controls the development of invariant natural killer T cell effector functions. Nat Immunol 9(9):1055–1064

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Savage AK et al (2008) The transcription factor PLZF directs the effector program of the NKT cell lineage. Immunity 29(3):391–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Wang H, Hogquist KA (2018) CCR7 defines a precursor for murine iNKT cells in thymus and periphery. Elife 7:e34793. https://doi.org/10.7554/eLife.34793.008

    Article  PubMed  PubMed Central  Google Scholar 

  76. Thiault N et al (2015) Peripheral regulatory T lymphocytes recirculating to the thymus suppress the development of their precursors. Nat Immunol 16(6):628–634

    Article  CAS  PubMed  Google Scholar 

  77. Cowan JE et al (2016) CCR7 controls thymus recirculation, but not production and emigration, of Foxp3(+) T Cells. Cell Rep 14(5):1041–1048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Legoux F et al (2019) Microbial metabolites control the thymic development of mucosal-associated invariant T cells. Science 366(6464):494–499

    Article  CAS  PubMed  Google Scholar 

  79. Nakajima A et al (2017) Maternal high fiber diet during pregnancy and lactation influences regulatory T cell differentiation in offspring in mice. J Immunol 199(10):3516–3524

    Article  CAS  PubMed  Google Scholar 

  80. Zegarra-Ruiz DF et al (2021) Thymic development of gut-microbiota-specific T cells. Nature 594(7863):413–417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Nakajima A et al (2014) Commensal bacteria regulate thymic Aire expression. PLoS ONE 9(8):e105904

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  82. Hikosaka Y et al (2008) The cytokine RANKL produced by positively selected thymocytes fosters medullary thymic epithelial cells that express autoimmune regulator. Immunity 29(3):438–450

    Article  CAS  PubMed  Google Scholar 

  83. White AJ et al (2014) An essential role for medullary thymic epithelial cells during the intrathymic development of invariant NKT cells. J Immunol 192(6):2659–2666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Roberts NA et al (2012) Rank signaling links the development of invariant gammadelta T cell progenitors and Aire(+) medullary epithelium. Immunity 36(3):427–437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Martinic MM et al (2017) The bacterial peptidoglycan-sensing molecules NOD1 and NOD2 promote CD8(+) thymocyte selection. J Immunol 198(7):2649–2660

    Article  CAS  PubMed  Google Scholar 

  86. Varian BJ et al (2016) Beneficial bacteria inhibit cachexia. Oncotarget 7(11):11803–11816

    Article  PubMed  PubMed Central  Google Scholar 

  87. Varian BJ et al (2017) Microbial lysate upregulates host oxytocin. Brain Behav Immun 61:36–49

    Article  CAS  PubMed  Google Scholar 

  88. Ojetti V et al (2014) The effect of Lactobacillus reuteri supplementation in adults with chronic functional constipation: a randomized, double-blind, placebo-controlled trial. J Gastrointest Liver Dis 23(4):387–391

    Article  Google Scholar 

  89. Hou C et al (2015) Study and use of the probiotic Lactobacillus reuteri in pigs: a review. J Anim Sci Biotechnol 6(1):14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  90. Amorosi S et al (2008) FOXN1 homozygous mutation associated with anencephaly and severe neural tube defect in human athymic Nude/SCID fetus. Clin Genet 73(4):380–384

    Article  CAS  PubMed  Google Scholar 

  91. Markert ML et al (2011) First use of thymus transplantation therapy for FOXN1 deficiency (nude/SCID): a report of 2 cases. Blood 117(2):688–696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Zuklys S et al (2016) Foxn1 regulates key target genes essential for T cell development in postnatal thymic epithelial cells. Nat Immunol 17(10):1206–1215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Nowell CS et al (2011) Foxn1 regulates lineage progression in cortical and medullary thymic epithelial cells but is dispensable for medullary sublineage divergence. PLoS Genet 7(11):e1002348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Ege MJ et al (2008) Prenatal exposure to a farm environment modifies atopic sensitization at birth. J Allergy Clin Immunol 122(2):407–412

    Article  PubMed  Google Scholar 

  95. Conrad ML et al (2009) Maternal TLR signaling is required for prenatal asthma protection by the nonpathogenic microbe Acinetobacter lwoffii F78. J Exp Med 206(13):2869–2877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Hu M et al (2019) Decreased maternal serum acetate and impaired fetal thymic and regulatory T cell development in preeclampsia. Nat Commun 10(1):3031

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Santner-Nanan B et al (2013) Fetal-maternal alignment of regulatory T cells correlates with IL-10 and Bcl-2 upregulation in pregnancy. J Immunol 191(1):145–153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Stokholm J et al (2017) Preeclampsia associates with asthma, allergy, and eczema in childhood. Am J Respir Crit Care Med 195(5):614–621

    Article  CAS  PubMed  Google Scholar 

  99. Byberg KK et al (2014) Birth after preeclamptic pregnancies: association with allergic sensitization and allergic rhinoconjunctivitis in late childhood; a historically matched cohort study. BMC Pediatr 14:101

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  100. Eviston DP et al (2012) Impaired fetal thymic growth precedes clinical preeclampsia: a case-control study. J Reprod Immunol 94(2):183–189

    Article  PubMed  Google Scholar 

  101. Eviston DP et al (2015) Altered fetal head growth in preeclampsia: a retrospective cohort proof-of-concept study. Front Pediatr 3:83

    PubMed  PubMed Central  Google Scholar 

  102. Owen DL et al (2019) Thymic regulatory T cells arise via two distinct developmental programs. Nat Immunol 20(2):195–205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Cui Y et al (2015) Mucosal-associated invariant T cell-rich congenic mouse strain allows functional evaluation. J Clin Invest 125(11):4171–4185

    Article  PubMed  PubMed Central  Google Scholar 

  104. Le Bourhis L et al (2010) Antimicrobial activity of mucosal-associated invariant T cells. Nat Immunol 11(8):701–708

    Article  PubMed  CAS  Google Scholar 

  105. Park SH et al (2000) Unaltered phenotype, tissue distribution and function of Valpha14(+) NKT cells in germ-free mice. Eur J Immunol 30(2):620–625

    Article  CAS  PubMed  Google Scholar 

  106. Wingender G et al (2012) Intestinal microbes affect phenotypes and functions of invariant natural killer T cells in mice. Gastroenterology 143(2):418–428

    Article  CAS  PubMed  Google Scholar 

  107. Yang Q, Bhandoola A (2016) The development of adult innate lymphoid cells. Curr Opin Immunol 39:114–120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Artis D, Spits H (2015) The biology of innate lymphoid cells. Nature 517(7534):293–301

    Article  CAS  PubMed  Google Scholar 

  109. Eberl G et al (2015) The brave new world of innate lymphoid cells. Nat Immunol 16(1):1–5

    Article  CAS  PubMed  Google Scholar 

  110. Constantinides MG et al (2014) A committed precursor to innate lymphoid cells. Nature 508(7496):397–401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Prince AL et al (2014) Innate PLZF+CD4+ alphabeta T cells develop and expand in the absence of Itk. J Immunol 193(2):673–687

    Article  CAS  PubMed  Google Scholar 

  112. Xu W et al (2019) An Id2(RFP)-reporter mouse redefines innate lymphoid cell precursor potentials. Immunity 50(4):1054-1068 e3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Pronovost GN, Hsiao EY (2019) Perinatal interactions between the microbiome, immunity, and neurodevelopment. Immunity 50(1):18–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Gury-BenAri M et al (2016) The spectrum and regulatory landscape of intestinal innate lymphoid cells are shaped by the microbiome. Cell 166(5):1231-1246 e3

    Article  CAS  PubMed  Google Scholar 

  115. Sanos SL et al (2009) RORgammat and commensal microflora are required for the differentiation of mucosal interleukin 22-producing NKp46+ cells. Nat Immunol 10(1):83–91

    Article  CAS  PubMed  Google Scholar 

  116. Satoh-Takayama N et al (2008) Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense. Immunity 29(6):958–970

    Article  CAS  PubMed  Google Scholar 

  117. Yin CC et al (2013) The Tec kinase ITK regulates thymic expansion, emigration, and maturation of gammadelta NKT cells. J Immunol 190(6):2659–2669

    Article  CAS  PubMed  Google Scholar 

  118. Liao XC, Littman DR (1995) Altered T cell receptor signaling and disrupted T cell development in mice lacking Itk. Immunity 3(6):757–769

    Article  CAS  PubMed  Google Scholar 

  119. Yang Y et al (2018) gammadelta T cells: crosstalk between microbiota, chronic inflammation, and colorectal cancer. Front Immunol 9:1483

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  120. Raviola E, Karnovsky MJ (1972) Evidence for a blood-thymus barrier using electron-opaque tracers. J Exp Med 136(3):466–498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Uchimura Y et al (2018) Antibodies set boundaries limiting microbial metabolite penetration and the resultant mammalian host response. Immunity 49(3):545-559 e5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Kyewski BA et al (1984) Intrathymic presentation of circulating non-major histocompatibility complex antigens. Nature 308(5955):196–199

    Article  CAS  PubMed  Google Scholar 

  123. Atibalentja DF et al (2009) Thymus-blood protein interactions are highly effective in negative selection and regulatory T cell induction. J Immunol 183(12):7909–7918

    Article  CAS  PubMed  Google Scholar 

  124. Drumea-Mirancea M et al (2006) Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. J Cell Sci 119(Pt 7):1396–1405

    Article  CAS  PubMed  Google Scholar 

  125. Murphy KM et al (1990) Induction by antigen of intrathymic apoptosis of CD4+CD8+TCRlo thymocytes in vivo. Science 250(4988):1720–1723

    Article  CAS  PubMed  Google Scholar 

  126. Volkmann A et al (1997) Antigen-presenting cells in the thymus that can negatively select MHC class II-restricted T cells recognizing a circulating self antigen. J Immunol 158(2):693–706

    CAS  PubMed  Google Scholar 

  127. Liblau RS et al (1996) Intravenous injection of soluble antigen induces thymic and peripheral T-cells apoptosis. Proc Natl Acad Sci USA 93(7):3031–3036

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Zhang H et al (2017) A distinct subset of plasmacytoid dendritic cells induces activation and differentiation of B and T lymphocytes. Proc Natl Acad Sci USA 114(8):1988–1993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Hadeiba H et al (2012) Plasmacytoid dendritic cells transport peripheral antigens to the thymus to promote central tolerance. Immunity 36(3):438–450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Ito T et al (2006) Specialization, kinetics, and repertoire of type 1 interferon responses by human plasmacytoid predendritic cells. Blood 107(6):2423–2431

    Article  CAS  PubMed  Google Scholar 

  131. Barchet W et al (2002) Virus-induced interferon alpha production by a dendritic cell subset in the absence of feedback signaling in vivo. J Exp Med 195(4):507–516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Wurbel MA et al (2001) Mice lacking the CCR9 CC-chemokine receptor show a mild impairment of early T- and B-cell development and a reduction in T-cell receptor gammadelta(+) gut intraepithelial lymphocytes. Blood 98(9):2626–2632

    Article  CAS  PubMed  Google Scholar 

  133. Uehara S et al (2002) A role for CCR9 in T lymphocyte development and migration. J Immunol 168(6):2811–2819

    Article  CAS  PubMed  Google Scholar 

  134. Hadeiba H et al (2008) CCR9 expression defines tolerogenic plasmacytoid dendritic cells able to suppress acute graft-versus-host disease. Nat Immunol 9(11):1253–1260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Hanabuchi S et al (2010) Thymic stromal lymphopoietin-activated plasmacytoid dendritic cells induce the generation of FOXP3+ regulatory T cells in human thymus. J Immunol 184(6):2999–3007

    Article  CAS  PubMed  Google Scholar 

  136. Proietto AI et al (2008) Dendritic cells in the thymus contribute to T-regulatory cell induction. Proc Natl Acad Sci U S A 105(50):19869–19874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Proietto AI et al (2009) The impact of circulating dendritic cells on the development and differentiation of thymocytes. Immunol Cell Biol 87(1):39–45

    Article  CAS  PubMed  Google Scholar 

  138. Hapfelmeier S et al (2008) Microbe sampling by mucosal dendritic cells is a discrete, MyD88-independent step in DeltainvG S. Typhimurium colitis. J Exp Med 205(2):437–450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Niess JH et al (2005) CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science 307(5707):254–258

    Article  CAS  PubMed  Google Scholar 

  140. Voboril M et al (2020) Toll-like receptor signaling in thymic epithelium controls monocyte-derived dendritic cell recruitment and Treg generation. Nat Commun 11(1):2361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Brown EM et al (2013) The role of the immune system in governing host-microbe interactions in the intestine. Nat Immunol 14(7):660–667

    Article  CAS  PubMed  Google Scholar 

  142. Hooper LV et al (2012) Interactions between the microbiota and the immune system. Science 336(6086):1268–1273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Lathrop SK et al (2011) Peripheral education of the immune system by colonic commensal microbiota. Nature 478(7368):250–254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Cebula A et al (2013) Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota. Nature 497(7448):258–262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Greiling TM et al (2018) Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus. Sci Transl Med 10(434)

  146. Hebbandi Nanjundappa R et al (2017) A gut microbial mimic that hijacks diabetogenic autoreactivity to suppress colitis. Cell 171(3):655-667 e17

    Article  CAS  PubMed  Google Scholar 

  147. Gil-Cruz C et al (2019) Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy. Science 366(6467):881–886

    Article  CAS  PubMed  Google Scholar 

  148. Kita H et al (2002) Analysis of TCR antagonism and molecular mimicry of an HLA-A0201-restricted CTL epitope in primary biliary cirrhosis. Hepatology 36(4 Pt 1):918–926

    CAS  PubMed  Google Scholar 

  149. Bogdanos DP et al (2004) Microbial mimics are major targets of crossreactivity with human pyruvate dehydrogenase in primary biliary cirrhosis. J Hepatol 40(1):31–39

    Article  CAS  PubMed  Google Scholar 

  150. Ioannidis M et al (2020) The immune modulating properties of mucosal-associated invariant T cells. Front Immunol 11:1556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. McWilliam HE, Villadangos JA (2018) MR1 antigen presentation to MAIT cells: new ligands, diverse pathways? Curr Opin Immunol 52:108–113

    Article  CAS  PubMed  Google Scholar 

  152. Bernasconi P et al (2005) Increased toll-like receptor 4 expression in thymus of myasthenic patients with thymitis and thymic involution. Am J Pathol 167(1):129–139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Boursalian TE et al (2004) Continued maturation of thymic emigrants in the periphery. Nat Immunol 5(4):418–425

    Article  CAS  PubMed  Google Scholar 

  154. Hendricks DW, Fink PJ (2011) Recent thymic emigrants are biased against the T-helper type 1 and toward the T-helper type 2 effector lineage. Blood 117(4):1239–1249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Makaroff LE et al (2009) Postthymic maturation influences the CD8 T cell response to antigen. Proc Natl Acad Sci USA 106(12):4799–4804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Cunningham CA et al (2017) Cutting edge: defective aerobic glycolysis defines the distinct effector function in antigen-activated CD8(+) recent thymic emigrants. J Immunol 198(12):4575–4580

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This work was supported by the CIHR grant (PJT-156073) to M.B. Geuking.

Author information

Authors and Affiliations

Authors

Contributions

MBG and RHN contributed to conceptualization:. RHN, CSU, and MBG were involved in writing and editing.

Corresponding author

Correspondence to Markus B. Geuking.

Ethics declarations

Conflict of interest

The authors have no relevant financial and non-financial interests to disclose.

Ethics approval and consent to participate

Not applicable.

Consent to publication

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hebbandi Nanjundappa, R., Sokke Umeshappa, C. & Geuking, M.B. The impact of the gut microbiota on T cell ontogeny in the thymus. Cell. Mol. Life Sci. 79, 221 (2022). https://doi.org/10.1007/s00018-022-04252-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00018-022-04252-y

Keywords

Navigation