Trojan Horses and Black Queens: ‘causal core’ explanations in microbiome research


Lynch et al., in an article in this issue, argue that an entire microbiome is rarely, if ever, the right target of analysis for causal explanations in microbiome research. They argue, using interventionist criteria of proportionality, specificity and stability, for restricting causal claims to the smallest subset of microbes—a causal core—that generate the effect of interest. A further question remains: what kind of interactions generate a consortium of microbes that can operate as causal agents in this manner? Here I introduce two possible kinds of such consortia: ‘trojan horses’ and ‘syntrophic’ individuals.

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


  1. 1.

    The historical details used in this example come from Baird and Arroyo (2013).

  2. 2.

    This coining and account of individuals has been developed in conjunction with my coauthor and collaborator Leonardo Bich from the University of the Basque Country.


  1. Baird JD, Arroyo LG (2013) Historical aspects of Potomac horse fever in Ontario (1924–2010). Can Vet J 54:565–572

    Google Scholar 

  2. Doolittle WF, Booth A (2016) It’s the song, not the singer: an exploration of holobiosis and evolutionary theory. Biol Philos 32:5–24

    Article  Google Scholar 

  3. Fichorova RN et al (2012) Endobiont viruses sensed by the human host: beyond conventional antiparasitic therapy. PLoS ONE 7(11):e48418.

    Article  Google Scholar 

  4. Graves KJ et al (2019) Trichomonas vaginalis virus: a review of the literature. Int J STD AIDS 30:496–504

    Article  Google Scholar 

  5. Hall EK et al (2018) Understanding how microbiomes influence the systems they inhabit. Nat Microbiol 3:977–982

    Article  Google Scholar 

  6. Lynch KE, Parke EC, O’Malley MA (2019) How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biol Philos.

    Article  Google Scholar 

  7. Morris JJ et al (2012) The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio. Published online May 2, 2012.

  8. Morris JJ (2015) Black Queen evolution: the role of leakiness in structuring microbial communities. Trends Genet 31(8):475–482

    Article  Google Scholar 

  9. Skillings DJ (2016) Holobionts and the ecology of organisms: multi-species communities or integrated individuals? Biol Philos 31:875

    Article  Google Scholar 

  10. Valdivia RH, Heitman J (2007) Endosymbiosis: the evil within. Curr Biol 17(11):R408–R410

    Article  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Derek Skillings.

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

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Skillings, D. Trojan Horses and Black Queens: ‘causal core’ explanations in microbiome research. Biol Philos 34, 60 (2019).

Download citation


  • Interventionist causation
  • Syntrophy
  • Proportionality
  • Microbiome
  • Health
  • Disease