Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida.

Journal: Communications biology
PMID: 40251395

Abstract

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

Authors

  • Apostolos Zournas
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Matthew R Incha
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Tijana Radivojević
    DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
  • Vincent Blay
    Fisher College of Business , The Ohio State University , Gerlach Hall, 2108 Neil Avenue, Columbus , Ohio 43210 , United States.
  • Jose Manuel Martí
    Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
  • Zak Costello
    Joint BioEnergy Institute (JBEI) , Emeryville , California 94608 , United States.
  • Matthias Schmidt
    Institute of Protein Biochemistry, Ulm University, Ulm, Germany.
  • Tan Chung
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Mitchell G Thompson
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Allison Pearson
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Patrick C Kinnunen
    Department of Chemical Engineering, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI, 48109-2800, USA.
  • Thomas Eng
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Christopher E Lawson
    Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
  • Stephen Tan
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Tadeusz Ogorzalek
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Nurgul Kaplan
    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Mark Forrer
    Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA.
  • Tyler Backman
    Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States.
  • Aindrila Mukhopadhyay
    Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
  • Nathan J Hillson
    Joint BioEnergy Institute (JBEI) , Emeryville , California 94608 , United States.
  • Jay D Keasling
    Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs., Lyngby, Denmark.
  • Hector Garcia Martin
    Joint BioEnergy Institute (JBEI) , Emeryville , California 94608 , United States.

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