Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production

Gamble, C.; Bryant, D.; Carrieri, D.; Bixby, E.; Dang, J.; Marshall, J.; Doughty, D.; Colwell, L.; Berndl, M.; Roberts, J.; Frumkin, M.

doi:10.1101/2021.08.06.453272

bioRxiv · 10.1101/2021.08.06.453272

Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production

Gamble, C.·Bryant, D.·Carrieri, D.·Bixby, E.·Dang, J.·Marshall, J.·Doughty, D.·Colwell, L.·Berndl, M.·Roberts, J.·Frumkin, M.

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Abstract

BackgroundArthrospira platensis (commonly known as spirulina) is a promising new platform for low-cost manufacturing of biopharmaceuticals. However, full realization of the platforms potential will depend on achieving both high growth rates of spirulina and high expression of therapeutic proteins. ObjectiveWe aimed to optimize culture conditions for the spirulina-based production of therapeutic proteins. MethodsWe used a machine learning approach called Bayesian black-box optimization to iteratively guide experiments in 96 photobioreactors that explored the relationship between production outcomes and 17 environmental variables such as pH, temperature, and light intensity. ResultsOver 16 rounds of experiments, we identified key variable adjustments that approximately doubled spirulina-based production of heterologous proteins, improving volumetric productivity between 70% to 100% in multiple bioreactor setting configurations. ConclusionAn adaptive, machine learning-based approach to optimize heterologous protein production can improve outcomes based on complex, multivariate experiments, identifying beneficial variable combinations and adjustments that might not otherwise be discoverable within high-dimensional data.

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Gamble, C., Bryant, D., Carrieri, D., Bixby, E., Dang, J., Marshall, J., Doughty, D., Colwell, L., Berndl, M., Roberts, J., Frumkin, M.. 2021-08-08. Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production. https://doi.org/10.1101/2021.08.06.453272

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