Biology & Philosophy

, 35:1 | Cite as

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

  • Gregor P. GreslehnerEmail author
  • Maël Lemoine
Part of the following topical collections:
  1. Target Article: How Causal are Microbiomes


In our commentary on Lynch et al.’s target paper (Biol Philos, 2019., 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.


Microbiome Causality Decomposition Phenotype 



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).


  1. Bourrat P (2018) Have causal claims about the gut microbiome been over-hyped? BioEssays 40(12):1800178. CrossRefGoogle 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. CrossRefGoogle Scholar
  3. Ellegaard KM, Engel P (2016) Beyond 16S rRNA community profiling: Intra-species diversity in the gut microbiota. Front Microbiol 7:1475. CrossRefGoogle 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. CrossRefGoogle Scholar
  5. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70. CrossRefGoogle Scholar
  6. Huneman P (2010) Topological explanations and robustness in biological sciences. Synthese 177(2):213–245. CrossRefGoogle Scholar
  7. Kostić D (2018) Mechanistic and topological explanations: an introduction. Synthese 195(1):1–10. CrossRefGoogle Scholar
  8. López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G (2013) The hallmarks of aging. Cell 153(6):1194–1217. CrossRefGoogle 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. CrossRefGoogle Scholar
  10. O’Malley MA, Skillings DJ (2018) Methodological strategies in microbiome research and their explanatory implications. Perspect Sci 26(2):239–265. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle Scholar
  13. Woodward J (2010) Causation in biology: stability, specificity, and the choice of levels of explanation. Biol Philos 25(3):287–318. CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.ImmunoConcept, UMR5164, CNRSUniversity of BordeauxBordeauxFrance

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