EcoFAB: Advancing microbiome science through standardized fabricated ecosystems

Published

June 21, 2019

Author(s)

Karsten Zengler, Kirsten Hofmockel, Scott Behie, Hans Bernstein, James Brown, Jos? Dinneny, Sheri Floge, Samuel Forry, Matthias Hess, Scott Jackson, Stephen Lindemann, Jennifer Pett-Ridge, Elizabeth Shank, Ophelia Venturelli, Matthew Wallenstein, Nitin Baliga, Christer Jansson, Trent Northen

Abstract

Microbiome science is arguably the fastest-advancing research field in biology today. However, current efforts are largely focused on disparate and often irreproducible experimental systems. Here we present the results of a one-and-a-half-day workshop that brought together over 60 thought leaders in microbial genomics, systems biology, microbial ecology, plant biology, and ioinformatics to discuss potential approaches for the development of standardized model ecosystems and methods of analyses for microbiome research. This group developed a roadmap to advance and integrate efforts to fabricate model microbial ecosystems (EcoFABs) that will serve as standardized experimental platforms to study microbial community ecology in laboratory settings. The development of generally applicable, reproducible, and easily disseminated EcoFABs that capture important aspects of native microbial ecosystems hold great promise for advancing microbiome science. Generation and adoption of model ecosystems, akin to model organisms, will accelerate our predictive understanding of microbiomes via reproducible interrogation of interactions in controlled, perturbed, and replicated experiments. Achieving this vision will require both organization and coordination of new communities of microbiome scientists charged with validating designs and protocols, facilitating EcoFAB dissemination, and establishing data standards.

Citation

Nature Methods

Pub Type

Journals

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

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Keywords

Microbial, community, microbiome, model system, reproducibility, protocols

Citation

Zengler, K. , Hofmockel, K. , Behie, S. , Bernstein, H. , Brown, J. , Dinneny, J. , Floge, S. , Forry, S. , Hess, M. , Jackson, S. , Lindemann, S. , Pett-Ridge, J. , Shank, E. , Venturelli, O. , Wallenstein, M. , Baliga, N. , Jansson, C. and Northen, T. (2019), EcoFAB: Advancing microbiome science through standardized fabricated ecosystems, Nature Methods, [online], https://doi.org/10.1038/s41592-019-0465-0, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=927926 (Accessed May 21, 2026)

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