Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

The microenvironment of injured murine gut elicits a local pro-restitutive microbiota


The mammalian intestine houses a complex microbial community, which influences normal epithelial growth and development, and is integral to the repair of damaged intestinal mucosa13. Restitution of injured mucosa involves the recruitment of immune cells, epithelial migration and proliferation4,5. Although microenvironmental alterations have been described in wound healing6, a role for extrinsic influences, such as members of the microbiota, has not been reported. Here, we show that a distinct subpopulation of the normal mucosal-associated gut microbiota expands and preferentially colonizes sites of damaged murine mucosa in response to local environmental cues. Our results demonstrate that formyl peptide receptor 1 (FPR1) and neutrophilic NADPH oxidase (NOX2) are required for the rapid depletion of microenvironmental oxygen and compensatory responses, resulting in a dramatic enrichment of an anaerobic bacterial consortium. Furthermore, the dominant member of this wound-mucosa-associated microbiota, Akkermansia muciniphila (an anaerobic, mucinophilic gut symbiont7,8), stimulated proliferation and migration of enterocytes adjacent to the colonic wounds in a process involving FPR1 and intestinal epithelial-cell-specific NOX1-dependent redox signalling. These findings thus demonstrate how wound microenvironments induce the rapid emergence of ‘probiont’ species that contribute to enhanced repair of mucosal wounds. Such microorganisms could be exploited as potential therapeutics.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Restitutive wound induces spatiotemporal change of wound mucosa-associated microbiota.
Figure 2: FPR1/NOX2 is required for microenvironmental changes in restitutive wounds, which promote anaerobic mucinophilic Akkermansia.
Figure 3: FPR1 is required for enrichment of Akkermansia sp.
Figure 4: Akkermansia muciniphila enhances redox-dependent wound restitution.

Similar content being viewed by others


  1. Hooper, L. V. et al. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291, 881–884 (2001).

    Article  Google Scholar 

  2. Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Host–bacterial mutualism in the human intestine. Science 307, 1915–1920 (2005).

    Article  Google Scholar 

  3. Pull, S. L., Doherty, J. M., Mills, J. C., Gordon, J. I. & Stappenbeck, T. S. Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc. Natl Acad. Sci. USA 102, 99–104 (2005).

    Article  Google Scholar 

  4. Lotz, M. M. et al. Intestinal epithelial restitution. Involvement of specific laminin isoforms and integrin laminin receptors in wound closure of a transformed model epithelium. Am. J. Pathol. 150, 747–760 (1997).

    Google Scholar 

  5. Miyoshi, H., Ajima, R., Luo, C. T., Yamaguchi, T. P. & Stappenbeck, T. S. Wnt5a potentiates TGFβ signaling to promote colonic crypt regeneration after tissue injury. Science 338, 108–113 (2012).

    Article  Google Scholar 

  6. Colgan, S. P., Curtis, V. F. & Campbell, E. L. The inflammatory tissue microenvironment in IBD. Inflamm. Bowel Dis. 19, 2238–2244 (2013).

    Article  Google Scholar 

  7. Derrien, M., Vaughan, E. E., Plugge, C. M. & de Vos, W. M. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 54, 1469–1476 (2004).

    Article  Google Scholar 

  8. Everard, A. et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc. Natl Acad. Sci. USA 110, 9066–9071 (2013).

    Article  Google Scholar 

  9. Alam, A. et al. Redox signaling regulates commensal-mediated mucosal homeostasis and restitution and requires formyl peptide receptor 1. Mucosal Immunol. 7, 645–655 (2014).

    Article  Google Scholar 

  10. Leoni, G. et al. Annexin A1, formyl peptide receptor, and NOX1 orchestrate epithelial repair. J. Clin. Invest. 123, 443–454 (2013).

    Article  Google Scholar 

  11. Seno, H. et al. Efficient colonic mucosal wound repair requires Trem2 signaling. Proc. Natl Acad. Sci. USA 106, 256–261 (2009).

    Article  Google Scholar 

  12. Johansson, M. E. et al. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc. Natl Acad. Sci. USA 105, 15064–15069 (2008).

    Article  Google Scholar 

  13. Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).

    Article  Google Scholar 

  14. Campbell, E. L. et al. Transmigrating neutrophils shape the mucosal microenvironment through localized oxygen depletion to influence resolution of inflammation. Immunity 40, 66–77 (2014).

    Article  Google Scholar 

  15. Wentworth, C. C., Alam, A., Jones, R. M., Nusrat, A. & Neish, A. S. Enteric commensal bacteria induce extracellular signal-regulated kinase pathway signaling via formyl peptide receptor-dependent redox modulation of dual specific phosphatase 3. J. Biol. Chem. 286, 38448–38455 (2011).

    Article  Google Scholar 

  16. Swanson, P. A. II et al. Enteric commensal bacteria potentiate epithelial restitution via reactive oxygen species-mediated inactivation of focal adhesion kinase phosphatases. Proc. Natl Acad. Sci. USA 108, 8803–8808 (2011).

    Article  Google Scholar 

  17. Jones, R. M. et al. Symbiotic lactobacilli stimulate gut epithelial proliferation via Nox-mediated generation of reactive oxygen species. EMBO J. 32, 3017–3028 (2013).

    Article  Google Scholar 

  18. Babbin, B. A. et al. Formyl peptide receptor-1 activation enhances intestinal epithelial cell restitution through phosphatidylinositol 3-kinase-dependent activation of Rac1 and Cdc42. J. Immunol. 179, 8112–8121 (2007).

    Article  Google Scholar 

  19. Reunanen, J. et al. Akkermansia muciniphila adheres to enterocytes and strengthens the integrity of epithelial cell layer. Appl. Environ. Microbiol. 81, 3655–3662 (2015).

    Article  Google Scholar 

  20. Derrien, M. et al. Modulation of mucosal immune response, tolerance, and proliferation in mice colonized by the mucin-degrader Akkermansia muciniphila. Front. Microbiol. 2, 166 (2011).

    Article  Google Scholar 

  21. Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J. & Knight, R. Error-correcting barcoded primers for pyrosequencing khundreds of samples in multiplex. Nature Methods 5, 235–237 (2008).

    Article  CAS  Google Scholar 

  22. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of abacteria and archaea. ISME J. 6, 610–618 (2012).

    Article  CAS  Google Scholar 

  23. Caporaso, J. G. et al. PyNAST: a flexible tool sfor aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2010).

    Article  CAS  Google Scholar 

  24. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: kcomputing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).

    Article  CAS  Google Scholar 

  25. Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).

    Article  CAS  Google Scholar 

  26. Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    Article  Google Scholar 

  27. Vaishnava, S. et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255–258 (2011).

    Article  CAS  Google Scholar 

  28. Derrien, M., Collado, M. C., Ben-Amor, K., Salminen, S. & de Vos, W. M. The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl. Environ. Microbiol. 74, 1646–1648 (2008).

    Article  CAS  Google Scholar 

  29. Pernthaler, J., Glöckner, F.-O., Schönhuber, W. & Amann, R. in Methods in Microbiology: Marine Microbiology Vol. 30 (ed. Paul, J.) 207–210 (Academic Press, 2001);

  30. Kundu, K. et al. Hydrocyanines: a class of fluorescent sensors that can image reactive oxygen species in cell culture, tissue, and in vivo. Angew. Chem. Int. Ed. Engl. 48, 299–303 (2009).

    Article  CAS  Google Scholar 

  31. Roopchand, D. E. et al. Dietary polyphenols promote growth of the gut bacterium Akkermansia muciniphila and attenuate high-fat diet-induced metabolic syndrome. Diabetes 64, 2847–2858 (2015).

    Article  CAS  Google Scholar 

Download references


The authors thank F. David, R. Isett, J. Taylor, H. Yi, M. Zwick and C. Kraft for helpful input. This work was supported by grants RO1DK089763 to A.S.N. and A.N., RO1DK055679 to A.N. and RO1AI64462 to A.S.N. A.A. is supported by a Career Development Award from the Crohn's and Colitis Foundation of America.

Author information

Authors and Affiliations



A.A., A.N. and A.S.N. conceptualized the study, directed the work and wrote the manuscript. A.A., G.L. A.N. and A.S.N. planned and analysed the experiments. R.M.J., A.A., G.L., M.Q., H.W., C.D. and H.N. performed the experiments.

Corresponding authors

Correspondence to Asma Nusrat or Andrew S. Neish.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1-8 and relative abundance of the bacterial genus as determined by HTS. (PDF 1379 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Alam, A., Leoni, G., Quiros, M. et al. The microenvironment of injured murine gut elicits a local pro-restitutive microbiota. Nat Microbiol 1, 15021 (2016).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:

This article is cited by


Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology