News & Views | Published:


Broad collateral damage of drugs against the gut microbiome

Nature Reviews Gastroenterology & Hepatologyvolume 15pages457458 (2018) | Download Citation

In a new study, Maier et al. reveal that non-antibiotic drugs intended to target human cells have off-target effects on the growth of human gut bacteria at clinically relevant concentrations. These results emphasize the need for a new field of metagenomic toxicology aimed at a more comprehensive understanding of the toxicity of compounds for humans and their associated microbial communities.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    National Center for Health Statistics. Therapeutic drug use. CDC (2017).

  2. 2.

    Spanogiannopoulos, P., Bess, E. N., Carmody, R. N. & Turnbaugh, P. J. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat. Rev. Microbiol. 14, 273–287 (2016).

  3. 3.

    Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560–564 (2016).

  4. 4.

    Wu, H. et al. Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nat. Med. 23, 850–858 (2017).

  5. 5.

    Maier, L. et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018).

  6. 6.

    Turnbaugh, P. J. Making millennial medicine more meta. mSystems 3, e00154–17 (2018).

  7. 7.

    Imhann, F. et al. Proton pump inhibitors affect the gut microbiome. Gut 65, 740–748 (2016).

  8. 8.

    Jackson, M. A. et al. Proton pump inhibitors alter the composition of the gut microbiota. Gut 65, 749–756 (2016).

  9. 9.

    Patterson, A. D. & Turnbaugh, P. J. Microbial determinants of biochemical individuality and their impact on toxicology and pharmacology. Cell Metab. 20, 761–768 (2014).

  10. 10.

    Blaser, M. J. The past and future biology of the human microbiome in an age of extinctions. Cell 172, 1173–1177 (2018).

Download references


P.J.T. is a Chan Zuckerberg Biohub Investigator and a Nadia’s Gift Foundation Innovator supported by the Damon Runyon Cancer Research Foundation (DRR-42-16), the NIH (R01HL122593) and the Searle Scholars Program (SSP-2016-1352). P.S. is supported by a Canadian Institutes of Health Research fellowship.

Author information


  1. Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA

    • Peter Spanogiannopoulos
    •  & Peter J. Turnbaugh
  2. Chan Zuckerberg Biohub, San Francisco, CA, USA

    • Peter J. Turnbaugh


  1. Search for Peter Spanogiannopoulos in:

  2. Search for Peter J. Turnbaugh in:

Competing interests

P.J.T. is on the scientific advisory board for Kaleido, Seres Therapeutics and WholeBiome. P.S. declares no competing interests.

Corresponding author

Correspondence to Peter J. Turnbaugh.

About this article

Publication history



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