Common principles and best practices for engineering microbiomes

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 a...

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Bibliographic Details
Published in:Nature reviews. Microbiology Vol. 17; no. 12; pp. 725 - 741
Main Authors: 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.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 01.12.2019
Nature Publishing Group
Springer Nature
Subjects:
631/326/252
631/326/2522
631/326/2565
631/326/2565/2134
631/326/41/2537
639/166/985
Agriculture
Agriculture - methods
Animal health
BASIC BIOLOGICAL SCIENCES
Best practice
Best practices
Bioelectric Energy Sources
Bioengineering
Bioengineering - methods
Biological Therapy - methods
Biomedical and Life Sciences
Biotechnology
Construction methods
Engineering
Environmental Microbiology
Guidelines as Topic
Humans
Infectious Diseases
Life Sciences
Medical Microbiology
Methods
Microbiological research
Microbiology
Microbiomes
Microbiota
Parasitology
Practice Guidelines as Topic
Principles
Review Article
Self-assembly
Virology
United States
ISSN:1740-1526, 1740-1534, 1740-1534
Online Access:Get full text
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Summary: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. Microbiome engineering has many potential applications, ranging from agriculture to medicine. In this Review, Lawson, McMahon and colleagues guide us through the design–build–test–learn cycle that has been successful in many disciplines and explain how it applies to microbiome engineering.
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SC0018409; AC02-05CH11231; CBET-1703504; MCB-1716594; GBMF5999; 1736255
USDOE Office of Science (SC), Biological and Environmental Research (BER)
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office
C.E.L. wrote the manuscript with direct input, edits, and critical feedback by all authors.
Author contributions
ISSN:1740-1526
1740-1534
1740-1534
DOI:10.1038/s41579-019-0255-9