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October 9, 2019

Nature paper proposes new research methods for microbiome engineering

Written By: Alex Holloway

Trina McMahon

The microbiome offers nearly limitless potential for research in areas from wastewater treatment to pharmaceutical drug production. University of Wisconsin-Madison engineers have published a paper encouraging colleagues to adopt common engineering methods to further microbiome research and development.

Katherine McMahon, a Vilas Distinguished Achievement Professor of Civil and Environmental Engineering, and Daniel Noguera, a Wisconsin Distinguished Professor of Civil and Environmental Engineering at UW-Madison, authored the paper, which was published in Nature Reviews Microbiology on Sept. 23.

Dan Noguera

In the paper, they propose microbiome engineering adopt an iterative design-build-test-learn (DBTL) cycle. The DBTL cycle is used in other sectors, such as manufacturing, metabolic engineering, and entrepreneurship, and McMahon and Noguera say in the paper it could “rapidly advance our ability to develop much needed tools and design concepts for harnessing microbiomes, delivering innovate solutions and advancing scientific knowledge.”

The cycle includes developing an initial design or model system to reach a defined goal; building the microbiome; testing its function against specified metric to determine whether the design-build solutions produced the objective; and learning what worked and what didn’t work to incorporate into subsequent DBTL processes.

Through proposing the use of the DBTL cycle, the McMahon and Noguera hope to promote a more rational, deliberate approach to creating microbiomes to maximize their utility.

Many of the ideas and initial collaborations for the paper were established during a May 2018 workshop at UW-Madison was sponsored by an award from the College of Engineering Research Innovation Committee, which was attended by microbiome research leaders from across the United States and abroad.