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Common principles and best practices for engineering microbiomes.

Christopher E Lawson1, William R Harcombe2, Roland Hatzenpichler3,4,5

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Harnessing Earth's microbiomes requires a structured approach. A design-build-test-learn (DBTL) cycle can advance microbiome engineering for medicine, agriculture, and environmental solutions.

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Area of Science:

  • Microbiology
  • Biotechnology
  • Synthetic Biology

Background:

  • Scientific interest in Earth's microbiomes is high, but knowledge gaps limit their application.
  • Efficiently utilizing microbiomes for societal and environmental challenges requires advanced engineering strategies.

Purpose of the Study:

  • To propose a design-build-test-learn (DBTL) cycle as a framework for microbiome engineering.
  • To outline generalizable approaches for microbiome design, construction, and analysis.
  • To identify challenges and opportunities in microbiome engineering for diverse applications.

Main Methods:

  • Reviewing key elements of an iterative DBTL cycle for microbiome engineering.
  • Focusing on top-down and bottom-up design, synthetic and self-assembled construction, and functional analysis tools.
  • Synthesizing best practices and guidelines for microbiome engineering.

Main Results:

  • The DBTL cycle provides a structured framework for advancing microbiome engineering.
  • Generalizable approaches for microbiome design and construction are presented.
  • Key challenges and opportunities across different engineering stages are discussed.

Conclusions:

  • Adoption of the DBTL framework will accelerate microbiome-based biotechnologies.
  • This approach will drive discoveries in fundamental microbiome science.
  • Applications span medicine, agriculture, energy, and environmental sectors, supporting the bioeconomy.