|
1
|
Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O'Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD. Common principles and best practices for engineering microbiomes. Nat Rev Microbiol 2019; 17:725-741. [PMID: 31548653 PMCID: PMC8323346 DOI: 10.1038/s41579-019-0255-9] [Citation(s) in RCA: 249] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
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.
Collapse
Affiliation(s)
- Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | | | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbra, CA, USA
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
| | - Héctor García Martín
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Agile BioFoundry, Emeryville, CA, USA
- Basque Center for Applied Mathematics, Bilbao, Spain
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ophelia S Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, Madison, WI, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
|
2
|
Okabe S, Kindaichi T, Ito T. MAR-FISH-An Ecophysiological Approach to Link Phylogenetic Affiliation and In Situ Metabolic Activity of Microorganisms at a Single-Cell Resolution. Microbes Environ 2004. [DOI: 10.1264/jsme2.19.83] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Satoshi Okabe
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University
| | - Tomonori Kindaichi
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University
| | - Tsukasa Ito
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University
| |
Collapse
|