EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Karsten Zengler; Kirsten Hofmockel; Nitin S Baliga; Scott W Behie; Hans C Bernstein; James B Brown; José R Dinneny; Sheri A Floge; Samuel P Forry; Matthias Hess; Scott A Jackson; Christer Jansson; Stephen R Lindemann; Jennifer Pett-Ridge; Costas Maranas; Ophelia S Venturelli; Matthew D Wallenstein; Elizabeth A Shank; Trent R Northen

doi:10.1038/s41592-019-0465-0

EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Nat Methods. 2019 Jul;16(7):567-571. doi: 10.1038/s41592-019-0465-0.

Authors

Karsten Zengler^{1

2}, Kirsten Hofmockel^{3

4}, Nitin S Baliga^{5

6

7}, Scott W Behie⁸, Hans C Bernstein^{9

10}, James B Brown^{11

12

13

14}, José R Dinneny¹⁵, Sheri A Floge^{16

17}, Samuel P Forry¹⁸, Matthias Hess¹⁹, Scott A Jackson¹⁸, Christer Jansson³, Stephen R Lindemann^{20

21}, Jennifer Pett-Ridge²², Costas Maranas²³, Ophelia S Venturelli²⁴, Matthew D Wallenstein²⁵, Elizabeth A Shank^{26

27}, Trent R Northen^{28

29}

Affiliations

¹ Department of Pediatrics, University of California, San Diego, CA, USA.
² Center for Microbiome Innovation, University of California, San Diego, CA, USA.
³ Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
⁴ Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA.
⁵ Institute for Systems Biology, Seattle, WA, USA.
⁶ Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA.
⁷ Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
⁸ Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
⁹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
¹⁰ The Norwegian College of Fishery Science and Arctic Centre for Sustainable Energy, UiT-The Arctic University of Norway, Tromsø, Norway.
¹¹ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹² Centre for Computational Biology, School of Biosciences, University of Birmingham, Birmingham, UK.
¹³ Statistics Department, University of California, Berkeley, Berkeley, CA, USA.
¹⁴ Preminon, LLC, Antioch, CA, USA.
¹⁵ Department of Biology, Stanford University, Stanford, CA, USA.
¹⁶ Department of Microbiology, The Ohio State University, Columbus, OH, USA.
¹⁷ Department of Biology, Wake Forest University, Winston-Salem, NC, USA.
¹⁸ Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
¹⁹ Department of Animal Science, University of California, Davis, Davis, CA, USA.
²⁰ Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA.
²¹ Department of Nutrition Science, Purdue University, West Lafayette, IN, USA.
²² Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
²³ Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
²⁴ Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
²⁵ Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
²⁶ Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
²⁷ Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
²⁸ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. trnorthen@lbl.gov.
²⁹ DOE Joint Genome Institute, Walnut Creek, CA, USA. trnorthen@lbl.gov.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Ecosystem*
Host Microbial Interactions
Humans
Microbiota*
Reproducibility of Results

Grants and funding

R35 GM124774/GM/NIGMS NIH HHS/United States