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Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells


Commensal gut bacteria impact the host immune system and can influence disease processes in several organs, including the brain. However, it remains unclear whether the microbiota has an impact on the outcome of acute brain injury. Here we show that antibiotic-induced alterations in the intestinal flora reduce ischemic brain injury in mice, an effect transmissible by fecal transplants. Intestinal dysbiosis alters immune homeostasis in the small intestine, leading to an increase in regulatory T cells and a reduction in interleukin (IL)-17–positive γδ T cells through altered dendritic cell activity. Dysbiosis suppresses trafficking of effector T cells from the gut to the leptomeninges after stroke. Additionally, IL-10 and IL-17 are required for the neuroprotection afforded by intestinal dysbiosis. The findings reveal a previously unrecognized gut-brain axis and an impact of the intestinal flora and meningeal IL-17+ γδ T cells on ischemic injury.

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Figure 1: Alteration of intestinal microbiota protects from MCAO-induced brain injury.
Figure 2: Increased Treg cells and reduced IL-17+ γδ T cells in the small intestine of ACSens mice.
Figure 3: Accumulation of IL-17+ γδ T cells at the meninges is associated with increased infarct size.
Figure 4: Migration of intestinal T cells to the meninges after ischemic brain injury.
Figure 5: Neuroprotection conferred by intestinal dysbiosis requires a reduction in intestinal IL-17+ γδ T cells.
Figure 6: DCs from ACSens mice originate in the intestine, induce Treg cells and downregulate IL-17+ γδ T cells in vitro.


  1. 1

    Henninger, N., Kumar, R. & Fisher, M. Acute ischemic stroke therapy. Expert Rev. Cardiovasc. Ther. 8, 1389–1398 (2010).

    PubMed  Google Scholar 

  2. 2

    Iadecola, C. & Anrather, J. The immunology of stroke: from mechanisms to translation. Nat. Med. 17, 796–808 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3

    Macrez, R. et al. Stroke and the immune system: from pathophysiology to new therapeutic strategies. Lancet Neurol. 10, 471–480 (2011).

    CAS  PubMed  Google Scholar 

  4. 4

    Mazmanian, S.K., Liu, C.H., Tzianabos, A.O. & Kasper, D.L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107–118 (2005).

    CAS  Google Scholar 

  5. 5

    Prinz, I., Silva-Santos, B. & Pennington, D.J. Functional development of γδ T cells. Eur. J. Immunol. 43, 1988–1994 (2013).

    CAS  PubMed  Google Scholar 

  6. 6

    Shichita, T. et al. Pivotal role of cerebral interleukin-17–producing γδ T cells in the delayed phase of ischemic brain injury. Nat. Med. 15, 946–950 (2009).

    CAS  PubMed  Google Scholar 

  7. 7

    Gelderblom, M. et al. Neutralization of the IL-17 axis diminishes neutrophil invasion and protects from ischemic stroke. Blood 120, 3793–3802 (2012).

    CAS  PubMed  Google Scholar 

  8. 8

    Liesz, A., Hu, X., Kleinschnitz, C. & Offner, H. Functional role of regulatory lymphocytes in stroke: facts and controversies. Stroke 46, 1422–1430 (2015).

    PubMed  PubMed Central  Google Scholar 

  9. 9

    Liesz, A. et al. Regulatory T cells are key cerebroprotective immunomodulators in acute experimental stroke. Nat. Med. 15, 192–199 (2009).

    CAS  PubMed  Google Scholar 

  10. 10

    Stubbe, T. et al. Regulatory T cells accumulate and proliferate in the ischemic hemisphere for up to 30 days after MCAO. J. Cereb. Blood Flow Metab. 33, 37–47 (2013).

    CAS  PubMed  Google Scholar 

  11. 11

    Li, P. et al. Adoptive regulatory T cell therapy protects against cerebral ischemia. Ann. Neurol. 74, 458–471 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Chaudhry, A. et al. CD4+ regulatory T cells control TH17 responses in a Stat3-dependent manner. Science 326, 986–991 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Huber, S. et al. TH17 cells express interleukin-10 receptor and are controlled by Foxp3 and Foxp3+ regulatory CD4+ T cells in an interleukin-10–dependent manner. Immunity 34, 554–565 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Park, S.-G. et al. T regulatory cells maintain intestinal homeostasis by suppressing γδ T cells. Immunity 33, 791–803 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Cho, S. et al. The class B scavenger receptor CD36 mediates free radical production and tissue injury in cerebral ischemia. J. Neurosci. 25, 2504–2512 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Kunz, A. et al. Neurovascular protection by ischemic tolerance: role of nitric oxide and reactive oxygen species. J. Neurosci. 27, 7083–7093 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Braniste, V. et al. The gut microbiota influences blood-brain barrier permeability in mice. Sci. Transl. Med. 6, 263ra158 (2014).

    PubMed  PubMed Central  Google Scholar 

  18. 18

    Hu, X., Li, P. & Chen, J. Pro: regulatory T cells are protective in ischemic stroke. Stroke 44, e85–e86 (2013).

    PubMed  Google Scholar 

  19. 19

    Round, J.L. & Mazmanian, S.K. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9, 313–323 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Nishio, J. & Honda, K. Immunoregulation by the gut microbiota. Cell. Mol. Life Sci. 69, 3635–3650 (2012).

    CAS  PubMed  Google Scholar 

  21. 21

    Justicia, C. et al. Neutrophil infiltration increases matrix metalloproteinase–9 in the ischemic brain after occlusion-reperfusion of the middle cerebral artery in rats. J. Cereb. Blood Flow Metab. 23, 1430–1440 (2003).

    CAS  PubMed  Google Scholar 

  22. 22

    Stowe, A.M. et al. Neutrophil elastase and neurovascular injury following focal stroke and reperfusion. Neurobiol. Dis. 35, 82–90 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Engelhardt, B. & Ransohoff, R.M. The ins and outs of T lymphocyte trafficking to the CNS: anatomical sites and molecular mechanisms. Trends Immunol. 26, 485–495 (2005).

    CAS  PubMed  Google Scholar 

  24. 24

    Morton, A.M. et al. Endoscopic photoconversion reveals unexpectedly broad leukocyte trafficking to and from the gut. Proc. Natl. Acad. Sci. USA 111, 6696–6701 (2014).

    CAS  PubMed  Google Scholar 

  25. 25

    Nowotschin, S. & Hadjantonakis, A.-K. Use of KikGR, a photoconvertible green-to-red fluorescent protein, for cell labeling and lineage analysis in ES cells and mouse embryos. BMC Dev. Biol. 9, 49 (2009).

    PubMed  PubMed Central  Google Scholar 

  26. 26

    Coombes, J.L. et al. A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-β– and retinoic acid–dependent mechanism. J. Exp. Med. 204, 1757–1764 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. 27

    Scott, C.L., Aumeunier, A.M. & Mowat, A.M. Intestinal CD103+ dendritic cells: master regulators of tolerance? Trends Immunol. 32, 412–419 (2011).

    CAS  PubMed  Google Scholar 

  28. 28

    Ochoa-Repáraz, J. et al. A polysaccharide from the human commensal Bacteroides fragilis protects against CNS demyelinating disease. Mucosal Immunol. 3, 487–495 (2010).

    PubMed  Google Scholar 

  29. 29

    Rescigno, M. et al. Dendritic cells express tight-junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nat. Immunol. 2, 361–367 (2001).

    CAS  PubMed  Google Scholar 

  30. 30

    Niess, J.H. et al. CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science 307, 254–258 (2005).

    CAS  PubMed  Google Scholar 

  31. 31

    Josefowicz, S.Z., Lu, L.-F. & Rudensky, A.Y. Regulatory T cells: mechanisms of differentiation and function. Annu. Rev. Immunol. 30, 531–564 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    Louveau, A. et al. Structural and functional features of central nervous system lymphatic vessels. Nature 523, 337–341 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Kleinschnitz, C. & Wiendl, H. Con: regulatory T cells are protective in ischemic stroke. Stroke 44, e87–e88 (2013).

    PubMed  Google Scholar 

  34. 34

    Kleinschnitz, C. et al. Regulatory T cells are strong promoters of acute ischemic stroke in mice by inducing dysfunction of the cerebral microvasculature. Blood 121, 679–691 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Roth, T.L. et al. Transcranial amelioration of inflammation and cell death after brain injury. Nature 505, 223–228 (2014).

    CAS  Google Scholar 

  36. 36

    Pérez-de-Puig, I. et al. Neutrophil recruitment to the brain in mouse and human ischemic stroke. Acta Neuropathol. 129, 239–257 (2015).

    PubMed  Google Scholar 

  37. 37

    Kleinschnitz, C. et al. Early detrimental T cell effects in experimental cerebral ischemia are neither related to adaptive immunity nor to thrombus formation. Blood 115, 3835–3842 (2010).

    CAS  PubMed  Google Scholar 

  38. 38

    Li, G.-Z. et al. Expression of interleukin-17 in ischemic brain tissue. Scand. J. Immunol. 62, 481–486 (2005).

    CAS  PubMed  Google Scholar 

  39. 39

    Kostulas, N., Pelidou, S.H., Kivisäkk, P., Kostulas, V. & Link, H. Increased IL-1β, IL-8 and IL-17 mRNA expression in blood mononuclear cells observed in a prospective ischemic stroke study. Stroke 30, 2174–2179 (1999).

    CAS  PubMed  Google Scholar 

  40. 40

    Erbel, C. et al. Expression of IL-17A in human atherosclerotic lesions is associated with increased inflammation and plaque vulnerability. Basic Res. Cardiol. 106, 125–134 (2011).

    CAS  PubMed  Google Scholar 

  41. 41

    Abraham, C. & Cho, J. Interleukin-23–TH17 pathways and inflammatory bowel disease. Inflamm. Bowel Dis. 15, 1090–1100 (2009).

    PubMed  Google Scholar 

  42. 42

    Keller, J.J. et al. Increased risk of stroke among patients with Crohn's disease: a population-based matched cohort study. Int. J. Colorectal Dis. 30, 645–653 (2015).

    PubMed  Google Scholar 

  43. 43

    Singh, S., Kullo, I.J., Pardi, D.S. & Loftus, E.V. Jr. Epidemiology, risk factors and management of cardiovascular diseases in IBD. Nat. Rev. Gastroenterol. Hepatol. 12, 26–35 (2015).

    PubMed  Google Scholar 

  44. 44

    Kilkenny, C., Browne, W., Cuthill, I.C., Emerson, M. & Altman, D.G. Animal research: reporting in vivo experiments—the ARRIVE guidelines. J. Cereb. Blood Flow Metab. 31, 991–993 (2011).

    PubMed  PubMed Central  Google Scholar 

  45. 45

    Ivanov, I.I. et al. Induction of intestinal TH17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Snel, J. et al. Comparison of 16S rRNA sequences of segmented filamentous bacteria isolated from mice, rats and chickens, and proposal of 'Candidatus arthromitus'. Int. J. Syst. Bacteriol. 45, 780–782 (1995).

    CAS  PubMed  Google Scholar 

  47. 47

    Barman, M. et al. Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract. Infect. Immun. 76, 907–915 (2008).

    CAS  PubMed  Google Scholar 

  48. 48

    Benson, A.K. et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl. Acad. Sci. USA 107, 18933–18938 (2010).

    CAS  PubMed  Google Scholar 

  49. 49

    Ubeda, C. et al. Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J. Exp. Med. 209, 1445–1456 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50

    Caricilli, A.M. et al. Gut microbiota is a key modulator of insulin resistance in Tlr2-knockout mice. PLoS Biol. 9, e1001212 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51

    Jackman, K., Kunz, A. & Iadecola, C. Modeling focal cerebral ischemia in vivo. Methods Mol. Biol. 793, 195–209 (2011).

    CAS  PubMed  Google Scholar 

  52. 52

    Lin, T.N., He, Y.Y., Wu, G., Khan, M. & Hsu, C.Y. Effect of brain edema on infarct volume in a focal cerebral ischemia model in rats. Stroke 24, 117–121 (1993).

    CAS  PubMed  Google Scholar 

  53. 53

    Bouët, V. et al. Sensorimotor and cognitive deficits after transient middle cerebral artery occlusion in the mouse. Exp. Neurol. 203, 555–567 (2007).

    PubMed  Google Scholar 

  54. 54

    Yagi, S. & Costanzo, R.M. Grafting the olfactory epithelium to the olfactory bulb. Am. J. Rhinol. Allergy 23, 239–243 (2009).

    PubMed  PubMed Central  Google Scholar 

  55. 55

    Jackman, K. et al. Progranulin deficiency promotes post-ischemic blood-brain barrier disruption. J. Neurosci. 33, 19579–19589 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. 56

    Schloss, P.D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57

    Buffie, C.G. et al. Precision microbiome reconstitution restores bile acid–mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).

    CAS  PubMed  Google Scholar 

  58. 58

    Sheneman, L., Evans, J. & Foster, J.A. Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22, 2823–2824 (2006).

    CAS  PubMed  Google Scholar 

  59. 59

    Garcia-Bonilla, L., Racchumi, G., Murphy, M., Anrather, J. & Iadecola, C. Endothelial CD36 contributes to postischemic brain injury by promoting neutrophil activation via CSF3. J. Neurosci. 35, 14783–14793 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Pino, P.A. & Cardona, A.E. Isolation of brain and spinal cord mononuclear cells using Percoll gradients. J. Vis. Exp. 48, 2348 (2011).

    Google Scholar 

  61. 61

    Roederer, M. Spectral compensation for flow cytometry: visualization artifacts, limitations and caveats. Cytometry 45, 194–205 (2001).

    CAS  PubMed  Google Scholar 

  62. 62

    Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002).

    Google Scholar 

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J.A. is the recipient of the Finbar and Marianne Kenny Research Scholarship. Parts of the study were supported by the US National Institutes of Health (NIH) grants NS081179 (J.A.) and NS34179 (C.I. and J.A.), the Feil Family Foundation (C.I.) and the Swiss National Science Foundation for Grants in Biology and Medicine (P3SMP3 148367; C.B.). We thank A.-K. Hadjantonakis (Memorial Sloan Kettering Cancer Center) for helpful discussions on the use of the KikGR33 mice.

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C.B. and D.B. contributed to study design, performed and/or contributed critically to all experiments and analyzed data. In some experiments, C.B. and D.B. were assisted by J.M., M.M., G.S. and G.R. G.F. performed EB extravasation experiments. E.G.P. and S.C. developed and provided the ACRes mouse model. L.L. performed r16S sequencing, and together with E.G.P., analyzed taxonomic data. C.I. contributed to study design. J.A. formulated the original hypothesis, designed the study, analyzed data and wrote the manuscript together with C.B., D.B. and C.I. All authors read and approved the manuscript.

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Correspondence to Josef Anrather.

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The authors declare no competing financial interests.

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Benakis, C., Brea, D., Caballero, S. et al. Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells. Nat Med 22, 516–523 (2016).

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