Active and machine learning-based approaches to rapidly enhance microbial chemical production

Metab Eng. 2021 Sep:67:216-226. doi: 10.1016/j.ymben.2021.06.009. Epub 2021 Jul 3.

Abstract

In order to make renewable fuels and chemicals from microbes, new methods are required to engineer microbes more intelligently. Computational approaches, to engineer strains for enhanced chemical production typically rely on detailed mechanistic models (e.g., kinetic/stoichiometric models of metabolism)-requiring many experimental datasets for their parameterization-while experimental methods may require screening large mutant libraries to explore the design space for the few mutants with desired behaviors. To address these limitations, we developed an active and machine learning approach (ActiveOpt) to intelligently guide experiments to arrive at an optimal phenotype with minimal measured datasets. ActiveOpt was applied to two separate case studies to evaluate its potential to increase valine yields and neurosporene productivity in Escherichia coli. In both the cases, ActiveOpt identified the best performing strain in fewer experiments than the case studies used. This work demonstrates that machine and active learning approaches have the potential to greatly facilitate metabolic engineering efforts to rapidly achieve its objectives.

Keywords: Active learning; Classification; Design of experiments; Machine learning; Metabolic engineering; Support vector machine.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Escherichia coli / genetics
  • Machine Learning*
  • Metabolic Engineering*
  • Phenotype