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Open AccessReview
Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions
by
Leonid A. Shaposhnikov
Leonid A. Shaposhnikov *
,
Aleksei S. Rozanov
Aleksei S. Rozanov * and
Alexey E. Sazonov
Alexey E. Sazonov
Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(15), 7483; https://doi.org/10.3390/ijms26157483 (registering DOI)
Submission received: 9 July 2025
/
Revised: 25 July 2025
/
Accepted: 31 July 2025
/
Published: 2 August 2025
Abstract
Lactic acid bacteria (LAB) are central to food, feed, and health biotechnology, yet their genomes have long resisted rapid, precise manipulation. This review charts the evolution of LAB genome-editing strategies from labor-intensive RecA-dependent double-crossovers to state-of-the-art CRISPR and CRISPR-associated transposase systems. Native homologous recombination, transposon mutagenesis, and phage-derived recombineering opened the door to targeted gene disruption, but low efficiencies and marker footprints limited throughput. Recent phage RecT/RecE-mediated recombineering and CRISPR/Cas counter-selection now enable scar-less point edits, seamless deletions, and multi-kilobase insertions at efficiencies approaching model organisms. Endogenous Cas9 systems, dCas-based CRISPR interference, and CRISPR-guided transposases further extend the toolbox, allowing multiplex knockouts, precise single-base mutations, conditional knockdowns, and payloads up to 10 kb. The remaining hurdles include strain-specific barriers, reliance on selection markers for large edits, and the limited host-range of recombinases. Nevertheless, convergence of phage enzymes, CRISPR counter-selection and high-throughput oligo recombineering is rapidly transforming LAB into versatile chassis for cell-factory and therapeutic applications.
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MDPI and ACS Style
Shaposhnikov, L.A.; Rozanov, A.S.; Sazonov, A.E.
Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions. Int. J. Mol. Sci. 2025, 26, 7483.
https://doi.org/10.3390/ijms26157483
AMA Style
Shaposhnikov LA, Rozanov AS, Sazonov AE.
Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions. International Journal of Molecular Sciences. 2025; 26(15):7483.
https://doi.org/10.3390/ijms26157483
Chicago/Turabian Style
Shaposhnikov, Leonid A., Aleksei S. Rozanov, and Alexey E. Sazonov.
2025. "Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions" International Journal of Molecular Sciences 26, no. 15: 7483.
https://doi.org/10.3390/ijms26157483
APA Style
Shaposhnikov, L. A., Rozanov, A. S., & Sazonov, A. E.
(2025). Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions. International Journal of Molecular Sciences, 26(15), 7483.
https://doi.org/10.3390/ijms26157483
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