Common principles and best practices for engineering microbiomes

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

doi:10.1038/s41579-019-0255-9

Common principles and best practices for engineering microbiomes

Journal Article · Mon Sep 23 00:00:00 EDT 2019 · Nature Reviews Microbiology

DOI:https://doi.org/10.1038/s41579-019-0255-9· OSTI ID:1579360

^[1]; ^[2]; ^[3]; ^[4]; ^[5]; ^[6]; ^[7]; ^[8]; Raskin, Lutgarde ^[9]; Venturelli, Ophelia S. ^[8]; ^[10]; Noguera, Daniel R. ^[11]; ^[8]

Univ. of Wisconsin-Madison, Madison, WI (United States); Unniversity of Wisconsin-Madison Department of Civil and Environmental Engineering
Univ. of Minnesota, Saint Paul, MN (United States)
Montana State Univ., Bozeman, MT (United States)
Purdue Univ., West Lafayette, IN (United States)
Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of California, Santa Barbara, CA (United States); DOE Joint Bioenergy Inst., Emeryville, CA (United States)
DOE Joint Bioenergy Inst., Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE Agile BioFoundry, Emeryville, CA (United States); Basque Center for Applied Mathematics, Bilbao (Spain)
Univ. of Wisconsin-Madison, Madison, WI (United States)
Univ. of Michigan, Ann Arbor, MI (United States)
Delft Univ. of Technology, Delft (Netherlands)
Univ. of Wisconsin-Madison, Madison, WI (United States); DOE Great Lakes Bioenergy Research Center, Madison, WI (United States)

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. Here, 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.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); USDOE Agile BioFoundry, Emeryville, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: Gordon and Betty Moore Foundation; National Science Foundation (NSF); Natural Sciences and Engineering Research Council of Canada (NSERC); Swiss National Science Foundation; USDOD; USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office; USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725; SC0018409

OSTI ID:: 1579360

Alternate ID(s):: OSTI ID: 1823327

Journal Information:: Nature Reviews Microbiology, Journal Name: Nature Reviews Microbiology Journal Issue: 12 Vol. 17; ISSN 1740-1526

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 10 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134781.v1	dataset	January 2020
Additional file 1 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134784.v1	dataset	January 2020
Additional file 2 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134787.v1	dataset	January 2020
Additional file 3 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134790	dataset	January 2020
Additional file 4 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134799	image	January 2020
Additional file 5 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134811	dataset	January 2020
Additional file 6 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134817	dataset	January 2020
Additional file 7 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134823.v1	dataset	January 2020
Additional file 8 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134829.v1	dataset	January 2020
Additional file 9 of Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes Huang, Kuo; Jiang, Qipeng; Liu, Liehua figshare https://doi.org/10.6084/m9.figshare.12134835	dataset	January 2020
Additional file 2 of Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle Palomo, Alejandro; Azevedo, Daniela; Touceda-Suárez, María figshare https://doi.org/10.6084/m9.figshare.20364002.v1	dataset	January 2022
Additional file 3 of Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle Palomo, Alejandro; Azevedo, Daniela; Touceda-Suárez, María figshare https://doi.org/10.6084/m9.figshare.20364005	dataset	January 2022
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