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EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Nature Methods volume 16, pages 567–571 (2019)Cite this article

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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.

Microorganisms are ubiquitous on Earth, and their activities are critical to the health and survival of all life. Highly complex microbial communities, consisting of hundreds to hundreds of thousands of different taxa, inhabit essentially all natural ecosystems. Within each ecosystem, these dynamic communities exhibit tremendous compositional and functional heterogeneity over time and space1,2. Although direct characterization of native microbiomes provides the most relevant data for understanding their biology and ecology, such studies are typically limited by their high cost, their limited replicability and the inability to use reductionistic technologies such as engineered microbes.

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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.

References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

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

    CAS  Google Scholar 

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

    Article  Google Scholar 

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

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Pediatrics, University of California, San Diego, CA, USA

    Karsten Zengler

  2. Center for Microbiome Innovation, University of California, San Diego, CA, USA

    Karsten Zengler

  3. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA

    Kirsten Hofmockel & Christer Jansson

  4. Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA

    Kirsten Hofmockel

  5. Institute for Systems Biology, Seattle, WA, USA

    Nitin S. Baliga

  6. Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA

    Nitin S. Baliga

  7. Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA

    Nitin S. Baliga

  8. Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA

    Scott W. Behie

  9. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

    Hans C. Bernstein

  10. The Norwegian College of Fishery Science and Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway

    Hans C. Bernstein

  11. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    James B. Brown & Trent R. Northen

  12. Centre for Computational Biology, School of Biosciences, University of Birmingham, Birmingham, UK

    James B. Brown

  13. Statistics Department, University of California, Berkeley, Berkeley, CA, USA

    James B. Brown

  14. Preminon, LLC, Antioch, CA, USA

    James B. Brown

  15. Department of Biology, Stanford University, Stanford, CA, USA

    José R. Dinneny

  16. Department of Microbiology, The Ohio State University, Columbus, OH, USA

    Sheri A. Floge

  17. Department of Biology, Wake Forest University, Winston-Salem, NC, USA

    Sheri A. Floge

  18. Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA

    Samuel P. Forry & Scott A. Jackson

  19. Department of Animal Science, University of California, Davis, Davis, CA, USA

    Matthias Hess

  20. Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA

    Stephen R. Lindemann

  21. Department of Nutrition Science, Purdue University, West Lafayette, IN, USA

    Stephen R. Lindemann

  22. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Jennifer Pett-Ridge

  23. Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA

    Costas Maranas

  24. Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA

    Ophelia S. Venturelli

  25. Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA

    Matthew D. Wallenstein

  26. Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Elizabeth A. Shank

  27. Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Elizabeth A. Shank

  28. DOE Joint Genome Institute, Walnut Creek, CA, USA

    Trent R. Northen

Authors
  1. Karsten Zengler
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  2. Kirsten Hofmockel
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  3. Nitin S. Baliga
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  4. Scott W. Behie
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  5. Hans C. Bernstein
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  6. James B. Brown
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  14. Jennifer Pett-Ridge
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  15. Costas Maranas
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  18. Elizabeth A. Shank
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  19. Trent R. Northen
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Contributions

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). https://doi.org/10.1038/s41592-019-0465-0

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