EcoFABs: advancing microbiome science through standardized fabricated ecosystems

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

doi:10.1038/s41592-019-0465-0

Title: EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Journal Article · 21 June 2019 · Nature Methods

DOI: https://doi.org/10.1038/s41592-019-0465-0 · OSTI ID:1526983

Zengler, Karsten ^[1]; Hofmockel, Kirsten ^[2]; Baliga, Nitin S. ^[3]; Behie, Scott W. ^[4]; Bernstein, Hans C. ^[5]; Brown, James B. ^[6]; Dinneny, José R. ^[7]; Floge, Sheri A. ^[8]; Forry, Samuel P. ^[9]; Hess, Matthias ^[10]; Jackson, Scott A. ^[9]; Jansson, Christer ^[11]; Lindemann, Stephen R. ^[12]; Pett-Ridge, Jennifer ^[13]; Maranas, Costas ^[14]; Venturelli, Ophelia S. ^[15]; Wallenstein, Matthew D. ^[16]; Shank, Elizabeth A. ^[17]; Northen, Trent R. ^[18]

Univ. of California, San Diego, CA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Iowa State Univ., Ames, IA (United States)
Inst. for Systems Biology, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States)
Univ. of California, Berkeley, CA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); The Arctic Univ. of Norway, Tromso (Norway)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Birmingham (United Kingdom); Univ. of California, Berkeley, CA (United States); Preminon LLC, Antioch, CA (United States)
Stanford Univ., CA (United States)
The Ohio State Univ., Columbus, OH (United States); Wake Forest Univ., Winston-Salem, NC (United States)
National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Univ. of California, Davis, CA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Purdue Univ., West Lafayette, IN (United States)
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Pennsylvania State Univ., University Park, PA (United States)
Univ. of Wisconsin, Madison, WI (United States)
Colorado State Univ., Fort Collins, CO (United States)
Univ. of North Carolina, Chapel Hill, NC (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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 here, will provide such model systems for microbiome studies.

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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Donald Danforth Plant Science Center, St. Louis, MO (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-07NA27344; AC05-000R22725; AC05-76RL01830; 1332344; 1804187; AC02-05CH11231; SC0018277; SC0012658; SC0012586; SC00138344; SC0013887

OSTI ID:: 1526983

Alternate ID(s):: OSTI ID: 1545155; OSTI ID: 1661029; OSTI ID: 1661054; OSTI ID: 2305665

Report Number(s):: LLNL-JRNL-757404; LLNL-JRNL-772061; 945176

Journal Information:: Nature Methods, Vol. 16, Issue 7; ISSN 1548-7091

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 53 works

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Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities Zuñiga, Cristal; Li, Chien-Ting; Yu, Geng Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0567-6	journal	October 2019
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Title: EcoFABs: advancing microbiome science through standardized fabricated ecosystems

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