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Title: EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Journal Article · · Nature Methods
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [9];  [11];  [12];  [13];  [14];  [15];  [16];  [17];  [18]
  1. Univ. of California, San Diego, CA (United States); Lawrence Berkeley National Laboratory
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Iowa State Univ., Ames, IA (United States)
  3. Institute for Systems Biology, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States)
  4. Univ. of California, Berkeley, CA (United States)
  5. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); UiT—The Arctic Univ. of Norway, Tromsø (Norway)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Birmingham, Birmingham (United Kingdom); Univ. of California, Berkeley, CA (United States)
  7. Stanford Univ., Stanford, CA (United States)
  8. The Ohio State Univ., Columbus, OH (United States); Wake Forest Univ., Winston-Salem, NC (United States)
  9. National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
  10. Univ. of California, Davis, CA (United States)
  11. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  12. Purdue Univ., West Lafayette, IN (United States)
  13. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  14. The Pennsylvania State Univ., University Park, PA (United States)
  15. Univ. of Wisconsin, Madison, WI (United States)
  16. Colorado State Univ., Fort Collins, CO (United States)
  17. Univ. of North Carolina, Chapel Hill, NC (United States)
  18. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
+ Show Author Affiliations

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

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231; SC0018277; SC0012658; SC0012586; SC0013887; AC05-76RL01830; AC52-07NA27344
OSTI ID:
1526983
Journal Information:
Nature Methods, Journal Name: Nature Methods Journal Issue: 7 Vol. 16; ISSN 1548-7091
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

References (28)

Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis journal April 2015
Model organisms — A historical perspective journal October 2010
Big questions, small worlds: microbial model systems in ecology journal April 2004
An obesity-associated gut microbiome with increased capacity for energy harvest journal December 2006
A communal catalogue reveals Earth’s multiscale microbial diversity journal November 2017
The role of ecological theory in microbial ecology journal May 2007
Symbiotic conversations are revealed under genetic interrogation journal October 2008
Core microbiomes for sustainable agroecosystems journal April 2018
A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities journal August 2017
The social network of microorganisms — how auxotrophies shape complex communities journal March 2018
Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip journal December 2015
Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel journal September 2016
Live imaging of root–bacteria interactions in a microfluidics setup journal March 2017
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice journal October 2017
The RootChip: An Integrated Microfluidic Chip for Plant Science journal December 2011
An in vitro model for the growth and analysis of chronic wound MRSA biofilms: C/DFR for the growth and analysis of MRSA biofilms journal September 2011
The President's Address journal April 1887
The development of Arabidopsis as a model plant journal March 2010
Metagenetics: spending our inheritance on the future journal March 2009
Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass journal January 2019
Microbial Biogeography: From Taxonomy to Traits journal May 2008
Communication among Oral Bacteria journal September 2002
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges journal May 2016
Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities journal October 2008
The microbiome quality control project: baseline study design and future directions journal December 2015
Research priorities for harnessing plant microbiomes in sustainable agriculture journal March 2017
Design of synthetic bacterial communities for predictable plant phenotypes journal February 2018
The struggle for existence, by G. F. Gause. book January 1934

Cited By (2)

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities journal October 2019
Common principles and best practices for engineering microbiomes journal September 2019

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