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Title: EcoFAB: Advancing microbiome science through standardized fabricated ecosystems

Abstract

The vital role microbiomes play in ecosystems and for human health is now apparent. Great progress has been made by using model systems to gain insight into host-microbe interactions, yet lack of standardized reproducible experimental systems and methods greatly limits microbiome science. Recent successes highlight the importance of developing these types of systems to deconstruct mechanisms mediating host-microbe interactions. Standardization of ‘fabricated ecosystems’ would enable detailed mechanistic interrogation and more effective knowledge transfer between researchers – analogous to the significant impact model organisms and cell systems have had in molecular and cell biology. To advance these efforts we advocate for strategies and overarching themes to enable communities of scientists to work together to develop standardized laboratory microbial consortia for studying host-associated microbiomes.

Authors:
 [1]; ORCiD logo [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [9];  [2];  [11];  [12];  [13];  [14];  [15];  [16];  [6]
  1. University of California
  2. BATTELLE (PACIFIC NW LAB)
  3. Unknwown
  4. University of California, Berkeley
  5. The Arctic University of Norway - Tromso, Norway
  6. Lawrence Berkeley National Laboratory
  7. Stanford University
  8. Ohio State University
  9. National Institute of Standards & Technology
  10. University of California, Davis
  11. PURDUE UNIVERSITY
  12. Lawrence Livermore National Laboratory
  13. Pennsylvania State University
  14. University of Wisconsin-Madison
  15. Colorado State University
  16. University of North Carolina at Chapel Hill
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1567192
Report Number(s):
PNNL-SA-138240
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 16; Journal Issue: 7
Country of Publication:
United States
Language:
English

Citation Formats

Zengler, Karsten, Hofmockel, Kirsten S., Baliga, Nitin S., Behie, Scott W., Bernstein, Hans, Brown, James B., Dinneny, Jose R., Floge, Sheri A., Forry, Samuel P., Hess, Matthias, Jackson, Scott A., Jansson, Georg C., Lindemann, Stephen R., Pett-Ridge, Jennifer, Maranas, Costas, Venturelli, Ophelia S., Wallenstein, Matthew D., Shank, Elizabeth A., and Northen, Trent R. EcoFAB: Advancing microbiome science through standardized fabricated ecosystems. United States: N. p., 2019. Web. doi:10.1038/s41592-019-0465-0.
Zengler, Karsten, Hofmockel, Kirsten S., Baliga, Nitin S., Behie, Scott W., Bernstein, Hans, Brown, James B., Dinneny, Jose R., Floge, Sheri A., Forry, Samuel P., Hess, Matthias, Jackson, Scott A., Jansson, Georg C., Lindemann, Stephen R., Pett-Ridge, Jennifer, Maranas, Costas, Venturelli, Ophelia S., Wallenstein, Matthew D., Shank, Elizabeth A., & Northen, Trent R. EcoFAB: Advancing microbiome science through standardized fabricated ecosystems. United States. doi:10.1038/s41592-019-0465-0.
Zengler, Karsten, Hofmockel, Kirsten S., Baliga, Nitin S., Behie, Scott W., Bernstein, Hans, Brown, James B., Dinneny, Jose R., Floge, Sheri A., Forry, Samuel P., Hess, Matthias, Jackson, Scott A., Jansson, Georg C., Lindemann, Stephen R., Pett-Ridge, Jennifer, Maranas, Costas, Venturelli, Ophelia S., Wallenstein, Matthew D., Shank, Elizabeth A., and Northen, Trent R. Wed . "EcoFAB: Advancing microbiome science through standardized fabricated ecosystems". United States. doi:10.1038/s41592-019-0465-0.
@article{osti_1567192,
title = {EcoFAB: Advancing microbiome science through standardized fabricated ecosystems},
author = {Zengler, Karsten and Hofmockel, Kirsten S. and Baliga, Nitin S. and Behie, Scott W. and Bernstein, Hans and Brown, James B. and Dinneny, Jose R. and Floge, Sheri A. and Forry, Samuel P. and Hess, Matthias and Jackson, Scott A. and Jansson, Georg C. and Lindemann, Stephen R. and Pett-Ridge, Jennifer and Maranas, Costas and Venturelli, Ophelia S. and Wallenstein, Matthew D. and Shank, Elizabeth A. and Northen, Trent R.},
abstractNote = {The vital role microbiomes play in ecosystems and for human health is now apparent. Great progress has been made by using model systems to gain insight into host-microbe interactions, yet lack of standardized reproducible experimental systems and methods greatly limits microbiome science. Recent successes highlight the importance of developing these types of systems to deconstruct mechanisms mediating host-microbe interactions. Standardization of ‘fabricated ecosystems’ would enable detailed mechanistic interrogation and more effective knowledge transfer between researchers – analogous to the significant impact model organisms and cell systems have had in molecular and cell biology. To advance these efforts we advocate for strategies and overarching themes to enable communities of scientists to work together to develop standardized laboratory microbial consortia for studying host-associated microbiomes.},
doi = {10.1038/s41592-019-0465-0},
journal = {Nature Methods},
number = 7,
volume = 16,
place = {United States},
year = {2019},
month = {7}
}