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.

Language, numeracy and logic in microbiome science

A Publisher Correction to this article was published on 12 June 2019

This article has been updated

To deliver precision therapeutics, microbiome-based medicine will require precision of language, logic and numerical accuracy. Epidemiological lessons of the past suggest that attempts to link almost everything in modern life with the microbiome as a risk factor for disease, without rapprochement with plausible mechanisms, will generate controversy rather than consensus.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Model demonstrating comparisons of abundance between microbiomes.

Change history

  • 12 June 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


  1. Gostin, L. O. Language, science, and politics: the politicization of public health. JAMA 319, 541–542 (2018).

    Article  Google Scholar 

  2. Parker, W. The “hygiene hypothesis” for allergic disease is a misnomer. BMJ 349, g5267 (2014).

    Article  Google Scholar 

  3. Bloomfield, S. F. et al. Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of target hygiene. Perspect. Public Health 136, 213–224 (2016).

    Article  Google Scholar 

  4. Orwell, G. Politics of the English language. University of Washington (1946).

  5. Hooks, K. B. & O’Malley, M. A. Dysbiosis and its discontents. mBio 8, e01492–17 (2017).

    Article  Google Scholar 

  6. Ma, B., Forney, L. J. & Ravel, J. Vaginal microbiome: rethinking health and disease. Annu. Rev. Microbiol. 66, 371–389 (2012).

    Article  CAS  Google Scholar 

  7. Barton, W. et al. The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut 67, 625–633 (2018).

    CAS  PubMed  Google Scholar 

  8. Hill, C. et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11, 506–514 (2014).

    Article  Google Scholar 

  9. Rosner, J. L. Ten times more microbial cells than body cells in humans? Microbe 9, 47 (2014).

    Google Scholar 

  10. Skrabanek, P. The emptiness of the black box. Epidemiology 5, 553–555 (1994).

    CAS  PubMed  Google Scholar 

Download references


F.S. and C.H. are supported, in part, by research grants from Science Foundation Ireland (SFI), including a centre grant (Number SFI/12/RC/227).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Fergus Shanahan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shanahan, F., Hill, C. Language, numeracy and logic in microbiome science. Nat Rev Gastroenterol Hepatol 16, 387–388 (2019).

Download citation

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

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