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Community structure follows simple assembly rules in microbial microcosms


Microorganisms typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals and humans they associate with. The ability to predict the structure of these complex communities is crucial to understanding and managing them. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. Our results demonstrate experimentally the ability of a simple bottom-up approach to predict community structure. Such an approach is key for anticipating the response of communities to changing environments, designing interventions to steer existing communities to more desirable states and, ultimately, rationally designing communities de novo.

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Figure 1: A bottom-up approach to predicting community composition from qualitative competitive outcomes.
Figure 2: Pairwise competitions resulted in stable coexistence or competitive exclusion.
Figure 3: Observed and predicted outcomes of trio competitions.
Figure 4: Survival in trio competitions is well predicted by pairwise outcomes.
Figure 5: Predicting survival in more diverse competition required incorporating the outcomes of the trio competitions.


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We thank A. Perez-Escudero, N. Vega, E. Yurtsev and members of the Gore Laboratory for critical discussions and comments on the manuscript. This work was supported by the Defense Advanced Research Projects Agency’s Biological Robustness in Complex Settings programme, an National Institutes of Health New Innovator Award (NIH DP2), an National Science Foundation CAREER Award, a Sloan Research Fellowship, the Pew Scholars Program and the Allen Investigator Program.

Author information




J.F. and J.G. designed the study. J.F. and L.M.H. performed the experiments and analysis. J.F., L.M.H. and J.G. wrote the manuscript.

Corresponding authors

Correspondence to Jonathan Friedman or Jeff Gore.

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The authors declare no competing financial interests.

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Supplementary Figures 1–8 and Supplementary Tables 1–3. (PDF 2112 kb)

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Friedman, J., Higgins, L. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat Ecol Evol 1, 0109 (2017).

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