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Review
. 2025 Aug;197(8):4897-4913.
doi: 10.1007/s12010-025-05260-x. Epub 2025 May 21.

Machine Learning Empowering Microbial Cell Factory: A Comprehensive Review

Dechun Kong  1 , Jinyi Qian  2 , Cong Gao  3 , Yuetong Wang  4 , Tianqiong Shi  5   6 , Chao Ye  7   8
Affiliations
Review

Machine Learning Empowering Microbial Cell Factory: A Comprehensive Review

Dechun Kong et al. Appl Biochem Biotechnol. 2025 Aug.

Abstract

The wide application of machine learning has provided more possibilities for biological manufacturing, and the combination of machine learning and synthetic biology technology has ignited even more brilliant sparks, which has created an unpredictable value for the upgrading of microbial cell factories. The review delves into the synergies between machine learning and synthetic biology to create research worth investigating in biotechnology. We explore relevant databases, toolboxes, and machine learning-derived models. Furthermore, we examine specific applications of this combined approach in chemical production, human health, and environmental remediation. By elucidating these successful integrations, this review aims to provide valuable guidance for future research at the intersection of biomanufacturing and artificial intelligence.

Keywords: Biomanufacturing; Database; Machine learning; Microbial cell factory; Synthetic biology; Toolbox.

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Conflict of interest statement

Declarations. Ethical Approval: This review did not involve animals or human subjects. Consent to Participate: Not applicable. Consent for Publication: Not applicable. Conflict of interest: The authors declare no competing interests.

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