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The theory of disappearing microbiota and the epidemics of chronic diseases


In recent decades, the incidence of many apparently unrelated chronic diseases has markedly increased. Here, I theorize that losses of particular bacterial species of our ancestral microbiota have altered the context in which immunological, metabolic and cognitive development occur in early life, which results in increased disease. This ominous trend suggests that we must refocus efforts to understand and reverse the underlying circumstances that are responsible for our disappearing microbiota.

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Figure 1: A model for the interaction of the inherited microbiota with early life immunological development in past and present children.


  1. Blaser, M. J. Who are we? Indigenous microbes and the ecology of human diseases. EMBO Rep. 7, 956–960 (2006).

    Article  CAS  Google Scholar 

  2. Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).

    Article  CAS  Google Scholar 

  3. Blaser, M. J. & Falkow, S. What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7, 887–894 (2009).

    Article  CAS  Google Scholar 

  4. Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016).

    Article  CAS  Google Scholar 

  5. Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108, 4554–4561 (2011).

    Article  CAS  Google Scholar 

  6. Bokulich, N. A. et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci. Transl. Med. 8, 343ra382 (2016).

    Article  Google Scholar 

  7. Cox, L. M. et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell 158, 705–721 (2014).

    Article  CAS  Google Scholar 

  8. Ruiz, V. E. et al. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. Nat. Comm. (in the press).

  9. Clemente, J. C. et al. The microbiome of uncontacted Amerindians. Sci. Adv. (2015).

  10. Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016).

    Article  CAS  Google Scholar 

  11. Simon, A. K., Hollander, G. A., McMichael, A. Evolution of the immune system in humans from infancy to old age. Proc. R. Soc. B 282, 20143085 (2015).

    Article  Google Scholar 

  12. Gomez de Agüero, M. et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).

    Article  Google Scholar 

  13. Gensollen, T., Iyer, S. S., Kasper, D. L. & Blumberg, R. S. How colonization by microbiota in early life shapes the immune system. Science 352, 539–544 (2016).

    Article  CAS  Google Scholar 

  14. Markle, J. G. et al. Sex differences in the gut microbiome drive hormone dependent regulation of autoimmunity. Science 339, 1084–1088 (2013).

    Article  CAS  Google Scholar 

  15. Livanos, A. E. et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat. Microbiol. 1, 16140 (2016).

    Article  CAS  Google Scholar 

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M.J.B. is supported, in part, by NIH grants U01AI22285 and R01DK090989, and by the Juvenile Diabetes Research Foundation and the C & D Fund.

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Correspondence to Martin J. Blaser.

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Blaser, M. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat Rev Immunol 17, 461–463 (2017).

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