Comment | Published:

The theory of disappearing microbiota and the epidemics of chronic diseases

Nature Reviews Immunology volume 17, pages 461463 (2017) | Download Citation


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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

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

  2. 2.

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

  3. 3.

    & What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7, 887–894 (2009).

  4. 4.

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

  5. 5.

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

  6. 6.

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

  7. 7.

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

  8. 8.

    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. 9.

    et al. The microbiome of uncontacted Amerindians. Sci. Adv. (2015).

  10. 10.

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

  11. 11.

    , , Evolution of the immune system in humans from infancy to old age. Proc. R. Soc. B 282, 20143085 (2015).

  12. 12.

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

  13. 13.

    , , & How colonization by microbiota in early life shapes the immune system. Science 352, 539–544 (2016).

  14. 14.

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

  15. 15.

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

Download references


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.

Author information


  1. Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, NY 10003, USA

    • Martin J. Blaser


  1. Search for Martin J. Blaser in:

Competing interests

The author declares no competing financial interests.

Corresponding author

Correspondence to Martin J. Blaser.

About this article

Publication history



Further reading

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