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Biology & Philosophy

, 34:62 | Cite as

How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers

  • Kate E. LynchEmail author
  • Emily C. Parke
  • Maureen A. O’Malley
Article
Part of the following topical collections:
  1. Target Article: How Causal are Microbiomes

Abstract

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made.

Keywords

Microbiome Causal explanation Helicobacter pylori Koch’s postulates Interventionism 

Notes

Acknowledgements

We thank Brett Calcott, Austen Ganley, David Kelley, John Matthewson, Sam Woolley, and the audience at PBDB 12 who provided crucial feedback on earlier versions of this manuscript, and acknowledge Pierrick Bourrat for earlier discussion of some of these ideas.

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Philosophy and Charles Perkins CentreUniversity of SydneySydneyAustralia
  2. 2.Department of Biological SciencesMacquarie UniversitySydneyAustralia
  3. 3.Philosophy, School of HumanitiesUniversity of AucklandAucklandNew Zealand
  4. 4.School of History and Philosophy of ScienceUniversity of SydneySydneyAustralia

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