Engineering Useful Microbial Species for Pharmaceutical Applications

Abstract

Microbial engineering has made a significant breakthrough in pharmaceutical biotechnology, greatly expanding the production of biologically active compounds, therapeutic proteins, and novel drug candidates. Recent advancements in genetic engineering, synthetic biology, and adaptive evolution have contributed to the optimization of microbial strains for pharmaceutical applications, playing a crucial role in enhancing their productivity and stability. The CRISPR-Cas system is widely utilized as a precise genome modification tool, enabling the enhancement of metabolite biosynthesis and the activation of synthetic biological pathways. Additionally, synthetic biology approaches allow for the targeted design of microorganisms with improved metabolic efficiency and therapeutic potential, thereby accelerating the development of new pharmaceutical products. The integration of artificial intelligence (AI) and machine learning (ML) plays a vital role in further advancing microbial engineering by predicting metabolic network interactions, optimizing bioprocesses, and accelerating the drug discovery process. However, challenges such as the efficient optimization of metabolic pathways, ensuring sustainable industrial-scale production, and meeting international regulatory requirements remain critical barriers in the field. Furthermore, to mitigate potential risks, it is essential to develop stringent biocontainment strategies and implement appropriate regulatory oversight. This review comprehensively examines recent innovations in microbial engineering, analyzing key technological advancements, regulatory challenges, and future development perspectives.

Keywords: artificial intelligence; biopharmaceuticals; machine learning; microbial engineering; synthetic biology.

Figure 1

Application of CRISPR-Cas9 in engineering microorganisms for pharmaceuticals. (1) The sgRNA (single guide RNA) binds to the Cas9 enzyme. (2) The bound guide RNA and Cas9 enzyme search for the target DNA sequence within the cell. (3) The Cas9 enzyme unwinds the DNA and uses the guide RNA to identify the matching nucleotide sequence. (4) Cas9 introduces a double-strand break (DSB) at the target DNA site. (5) After the double-strand break, DNA repair mechanisms introduce the desired genetic modifications by incorporating an inserted sequence (in red), which is delivered via a donor DNA template through homologous recombination or non-homologous end joining. The efficiency of insertion can be affected by the size of the inserted sequence, with larger inserts generally being less efficient. (6) The genetically modified microorganisms are cultured, and their successful genetic alterations are verified. (7) These engineered microorganisms are utilized for pharmaceutical applications. Created with BioRender, License No. A12H414.

Figure 2

Integration of advanced technologies in microbial engineering for pharmaceutical applications. Genetic engineering, synthetic biology, and adaptive evolution, combined with AI and ML methods, enable the optimization of microbial strains, the comprehensive analysis of genetic data, and the advancement of drug discovery technologies. These approaches open new opportunities for the identification and production of highly effective therapeutic compounds, such as antibiotics, biopharmaceuticals, and vaccines. Created with BioRender, agreement No. PK27ZEC4QO.

Figure 3

Sources of microbial contamination in biopharmaceutical manufacturing [144,145]. Created with BioRender, agreement No. KV27WPI3T0.

Figure 4

Bioethics and regulatory considerations in the application of GEMs. The figure illustrates the role and potential of GEMs in antibiotic production. It also highlights their potential ecological risks, including ecosystem imbalance, impact on biodiversity, and environmental contamination. The importance of bioethical principles and regulatory mechanisms in ensuring the safe and sustainable application of these technologies is emphasized. Created with BioRender, agreement No. TL27WPHN14.