EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, which we term EcoFABs, will provide such model systems for microbiome studies.

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Fig. 1: Vision for fabricated model microbial ecosystems and their impact on microbiome science.
Fig. 2: Two example devices for analysis of microbial interactions.


  1. 1.

    Thompson, L. R. et al. Nature 551, 457–463 (2017).

    CAS  Article  Google Scholar 

  2. 2.

    Zengler, K. & Zaramela, L. S. Nat. Rev. Microbiol. 16, 383–390 (2018).

    CAS  Article  Google Scholar 

  3. 3.

    Muller, B. & Grossniklaus, U. J. Proteomics 73, 2054–2063 (2010).

    Article  Google Scholar 

  4. 4.

    Wimpenny, J. W. T. CRC Handbook of Laboratory Model Systems for Microbial Ecosystems (CRC Press, 1988).

  5. 5.

    Winogradsky, S. Arch. Sci. Biol. 3, 297–352 (1895).

    CAS  Google Scholar 

  6. 6.

    Dallinger, W. D. J. R. Microsc. Soc. 7, 184–199 (1887).

    Article  Google Scholar 

  7. 7.

    Gause, G. F. The Struggle for Existence (The Williams & Wilkins Company, 1934).

  8. 8.

    Kolenbrander, P. E. et al. Microbiol. Mol. Biol. R 66, 486–505 (2002).

    CAS  Article  Google Scholar 

  9. 9.

    Jessup, C. M. et al. Trends Ecol. Evol. 19, 189–197 (2004).

    Article  Google Scholar 

  10. 10.

    Wolfe, B. E. Msystems 3, 00161-17 (2018).

  11. 11.

    Welch, J. L. M., Hasegawa, Y., McNulty, N. P., Gordon, J. I. & Borisy, G. G. Proc. Natl Acad. Sci. USA 114, E9105–E9114 (2017).

    Article  Google Scholar 

  12. 12.

    Yano, J. M. et al. Cell 161, 264–276 (2015).

    CAS  Article  Google Scholar 

  13. 13.

    Turnbaugh, P. J. et al. Nature 444, 1027–1031 (2006).

    Article  Google Scholar 

  14. 14.

    Zhalnina, K., Zengler, K., Newman, D. & Northen, T. R. MBio 9, e01175-18 (2018).

  15. 15.

    Koornneef, M. & Meinke, D. Plant J. 61, 909–921 (2010).

    CAS  Article  Google Scholar 

  16. 16.

    Busby, P. E. et al. PLoS Biol. 15, e2001793 (2017).

    Article  Google Scholar 

  17. 17.

    McDonald, J. A. et al. J. Microbiol. Methods 95, 167–174 (2013).

  18. 18.

    Agostinho, A. M. et al. J. Appl. Microbiol. 111, 1275–1282 (2011).

    CAS  Article  Google Scholar 

  19. 19.

    Kim, H. J., Li, H., Collins, J. J. & Ingber, D. E. Proc. Natl Acad. Sci. USA 113, E7–E15 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    Cremer, J. et al. Proc. Natl Acad. Sci. USA 113, 11414–11419 (2016).

    CAS  Article  Google Scholar 

  21. 21.

    Blaser, M. J. et al. MBio 7, e00714–e00716 (2016).

    CAS  Article  Google Scholar 

  22. 22.

    Gao, J. et al. J. Vis. Exp. 134, e57170 (2018).

    Google Scholar 

  23. 23.

    Massalha, H., Korenblum, E., Malitsky, S., Shapiro, O. H. & Aharoni, A. Proc. Natl Acad. Sci. USA 114, 4549–4554 (2017).

    CAS  Article  Google Scholar 

  24. 24.

    Toju, H. et al. Nat. Plants 4, 247–257 (2018).

    Article  Google Scholar 

  25. 25.

    Herrera Paredes, S. et al. PLoS Biol. 16, e2003962 (2018).

    Article  Google Scholar 

  26. 26.

    Grossmann, G. et al. Plant Cell 23, 4234–4240 (2011).

    CAS  Article  Google Scholar 

  27. 27.

    Lambert, B. S. et al. Nat. Microbiol. 2, 1344–1349 (2017).

    CAS  Article  Google Scholar 

  28. 28.

    Handelsman, J. Microb. Biotechnol. 2, 138–139 (2009).

    Article  Google Scholar 

  29. 29.

    Green, J. L., Bohannan, B. J. & Whitaker, R. J. Science 320, 1039–1043 (2008).

    CAS  Article  Google Scholar 

  30. 30.

    Little, A. E. F., Robinson, C. J., Peterson, S. B., Raffa, K. E. & Handelsman, J. Annu. Rev. Microbiol. 62, 375–401 (2008).

    CAS  Article  Google Scholar 

  31. 31.

    Ruby, E. G. Nat. Rev. Microbiol. 6, 752–762 (2008).

    CAS  Article  Google Scholar 

  32. 32.

    Prosser, J. I. et al. Nat. Rev. Microbiol. 5, 384–392 (2007).

    CAS  Article  Google Scholar 

  33. 33.

    Sinha, R., Abnet, C. C., White, O., Knight, R. & Huttenhower, C. Genome Biol. 16, 276 (2015).

    Article  Google Scholar 

  34. 34.

    Sasse, J. et al. New Phytol. 222, 1149–1160 (2019).

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Material is based on work supported by the National Science Foundation under grants 1332344 and 1804187 (to K.Z.), the Trial Ecosystem Advancement for Microbiome Science and the Microbial Community Analysis and Functional Evaluation in Soils Programs at Lawrence Berkeley National Laboratory by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research Awards DE-AC02-05CH11231 (to T.R.N.), DE‐SC0018277 (to J.R.D.) and DE-SC0012658, DE-SC0012586, DE-SC00138344 (to K.Z.), DE-SC0013887 (to E.A.S.), the Center for Bioenergy Innovation (CBI), DE-AC05-000R22725 (to C.M.), by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research under contract DE-AC05-76RL01830 with Pacific Northwest National Laboratory through the iPASS and PREMIS Initiatives (to C.J.), and the Strategic Planning Support Activities Program of Lawrence Berkeley National Laboratory (to T.R.N.). Work at Lawrence Livermore National Laboratory (J.P.R.) was conducted under the auspices of Contract DE-AC52-07NA27344 and SCW1039. We thank P. Kim and Z. Rostomian for assistance in figure preparation, and D. Gilbert and J. Tanamachi for helpful comments.

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T.R.N. and K.Z. created the draft manuscript. All authors contributed substantially to the draft manuscript, including editing to incorporate diverse expertise and research perspectives. K.Z. and T.R.N. prepared the final text and figures.

Corresponding author

Correspondence to Trent R. Northen.

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Competing interests

T.R.N. is an inventor on a related patent application (US 15/963,887). M.D.W. is a founder and shareholder of Growcentia, Inc.

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Zengler, K., Hofmockel, K., Baliga, N.S. et al. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat Methods 16, 567–571 (2019).

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