Kobe University Team Develops Template-Free DNA Editing for Safer Probiotics

Researchers at Kobe University have introduced a new DNA editing technique that allows for precise genetic modifications in Lactobacillus strains without using template DNA from other organisms. This approach closely mimics natural genetic variation and has enabled the team to produce a strain that does not generate chemicals known to worsen diabetes.

Traditionally, humans have enhanced microorganisms for food production by selecting favorable variants for products like wine, yogurt, and natto. In recent years, direct genetic modification has offered more control but has faced criticism due to the use of DNA from unrelated species.  Nishida Keiji, senior author on the study published in Applied Microbiology and Biotechnology, notes, “As a consequence, using such transgenic techniques is not favorable for food products due to legislations being restrictive and social acceptance being low.”

To address these concerns, Nishida and his team developed a DNA base editing technology. “We have invented a DNA base editing technology named Target-AID, which is superior to conventional techniques such as CRISPR-Cas9 in several aspects. For example, CRISPR-Cas9 induces DNA breaks and often causes cell death, while our Target-AID inserts precise point mutations without such breaks.”

The team applied this method to two major Lactobacillus species used in dairy and pickle production, achieving nearly 100% efficiency in targeted genome edits. They demonstrated the technique’s potential by mutating a gene responsible for producing a diabetes-aggravating chemical, resulting in a strain that produces yogurt with less than a tenth of that compound.

Nishida explains, “The bacteria we produced are not subject to regulations concerning genetically modified organisms when used as foods, supplements, or medicines. We thus expect that they can be readily commercialized after appropriate safety confirmation.” The researchers also showed that multiple genes could be edited simultaneously, suggesting applications for both industry and basic research. Nishida envisions future probiotic products with health benefits such as supporting immunity and reducing the impact of lifestyle-related diseases.