A dual decomposition strategy of both microbial and phenotypic components for a better understanding of causal claims


In our commentary on Lynch et al.’s target paper (Biol Philos, 2019. https://doi.org/10.1007/s10539-019-9702-2), we focus on decomposition as a research strategy. We argue that not only the presumptive microbial causes but also their supposed phenotypic effects need to be decomposed relative to each other. Such a dual decomposition strategy ought to improve the way in which causal claims in microbiome research can be made and understood.

This is a preview of subscription content, log in to check access.

Fig. 1


  1. Bourrat P (2018) Have causal claims about the gut microbiome been over-hyped? BioEssays 40(12):1800178. https://doi.org/10.1002/bies.201800178

    Article  Google Scholar 

  2. Darden L (2013) Mechanisms versus causes in biology and medicine. In: Chao H-K, Chen S-T, Millstein RL (eds) Mechanism and causality in biology and economics. Springer, New York, pp 19–34. https://doi.org/10.1007/978-94-007-2454-9_2

    Google Scholar 

  3. Ellegaard KM, Engel P (2016) Beyond 16S rRNA community profiling: Intra-species diversity in the gut microbiota. Front Microbiol 7:1475. https://doi.org/10.3389/fmicb.2016.01475

    Article  Google Scholar 

  4. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R (2016) Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535:94–103. https://doi.org/10.1038/nature18850

    Article  Google Scholar 

  5. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70. https://doi.org/10.1016/S0092-8674(00)81683-9

    Article  Google Scholar 

  6. Huneman P (2010) Topological explanations and robustness in biological sciences. Synthese 177(2):213–245. https://doi.org/10.1007/s11229-010-9842-z

    Article  Google Scholar 

  7. Kostić D (2018) Mechanistic and topological explanations: an introduction. Synthese 195(1):1–10. https://doi.org/10.1007/s11229-016-1257-z

    Article  Google Scholar 

  8. López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G (2013) The hallmarks of aging. Cell 153(6):1194–1217. https://doi.org/10.1016/j.cell.2013.05.039

    Article  Google Scholar 

  9. Lynch KE, Parke EC, O’Malley MA (2019) How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biol Philos. https://doi.org/10.1007/s10539-019-9702-2

    Article  Google Scholar 

  10. O’Malley MA, Skillings DJ (2018) Methodological strategies in microbiome research and their explanatory implications. Perspect Sci 26(2):239–265. https://doi.org/10.1162/POSC_a_00274

    Article  Google Scholar 

  11. Pajunen P, Jousilahti P, Borodulin K, Harald K, Tuomilehto J, Salomaa V (2011) Body fat measured by a near-infrared interactance device as a predictor of cardiovascular events: the FINRISK’92 cohort. Obesity 19(4):848–852. https://doi.org/10.1038/oby.2010.236

    Article  Google Scholar 

  12. Parke EC, Calcott B, O’Malley MA (2018) A cautionary note for claims about the microbiome’s impact on the “self”. PLoS Biol 16(9):e2006654. https://doi.org/10.1371/journal.pbio.2006654

    Article  Google Scholar 

  13. Woodward J (2010) Causation in biology: stability, specificity, and the choice of levels of explanation. Biol Philos 25(3):287–318. https://doi.org/10.1007/s10539-010-9200-z

    Article  Google Scholar 

Download references


Many thanks to Thomas Pradeu and the ImmunoConcept group. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme—Grant Agreement No. 637647—IDEM (P.I.: Thomas Pradeu).

Author information



Corresponding author

Correspondence to Gregor P. Greslehner.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This comment refers to the article available at https://doi.org/10.1007/s10539-019-9702-2.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Greslehner, G.P., Lemoine, M. A dual decomposition strategy of both microbial and phenotypic components for a better understanding of causal claims. Biol Philos 35, 1 (2020). https://doi.org/10.1007/s10539-019-9708-9

Download citation


  • Microbiome
  • Causality
  • Decomposition
  • Phenotype