Common principles and best practices for engineering microbiomes

Christopher E Lawson; William R Harcombe; Roland Hatzenpichler; Stephen R Lindemann; Frank E Löffler; Michelle A O'Malley; Héctor García Martín; Brian F Pfleger; Lutgarde Raskin; Ophelia S Venturelli; David G Weissbrodt; Daniel R Noguera; Katherine D McMahon

doi:10.1038/s41579-019-0255-9

Common principles and best practices for engineering microbiomes

Nat Rev Microbiol. 2019 Dec;17(12):725-741. doi: 10.1038/s41579-019-0255-9. Epub 2019 Sep 23.

Authors

Christopher E Lawson¹, William R Harcombe², Roland Hatzenpichler^{3

4

5}, Stephen R Lindemann⁶, Frank E Löffler^{7

8}, Michelle A O'Malley^{9

10}, Héctor García Martín^{10

11

12

13}, Brian F Pfleger¹⁴, Lutgarde Raskin¹⁵, Ophelia S Venturelli^{14

16

17}, David G Weissbrodt¹⁸, Daniel R Noguera^{19

20}, Katherine D McMahon^{21

22}

Affiliations

¹ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA. c.e.lawson.87@gmail.com.
² Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA.
³ Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
⁴ Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
⁵ Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
⁶ Department of Food Sciences, Purdue University, West Lafayette, IN, USA.
⁷ Center for Environmental Biotechnology, University of Tennessee-Knoxville, Knoxville, TN, USA.
⁸ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
⁹ Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbra, CA, USA.
¹⁰ DOE Joint Bioenergy Institute, Emeryville, CA, USA.
¹¹ Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹² DOE Agile BioFoundry, Emeryville, CA, USA.
¹³ Basque Center for Applied Mathematics, Bilbao, Spain.
¹⁴ Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
¹⁵ Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA.
¹⁶ Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
¹⁷ Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
¹⁸ Department of Biotechnology, Delft University of Technology, Delft, Netherlands.
¹⁹ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
²⁰ DOE Great Lakes Bioenergy Research Center, Madison, WI, USA.
²¹ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA. kdmcmahon@wisc.edu.
²² Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA. kdmcmahon@wisc.edu.

Abstract

Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.

Publication types

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

MeSH terms

Agriculture / methods
Bioelectric Energy Sources
Bioengineering / methods*
Biological Therapy / methods
Environmental Microbiology
Guidelines as Topic
Humans
Microbiota*
Practice Guidelines as Topic*

Grants and funding

R35 GM124774/GM/NIGMS NIH HHS/United States