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A research team from Kobe University has successfully edited the DNA of Lactobacillus strains directly, eliminating the need for a template from other organisms. This innovative technique mimics natural genetic variation and has led to the creation of a strain that does not produce harmful chemicals associated with diabetes.
For centuries, humans have selectively bred microorganisms to enhance the production of various goods such as wine, yogurt, and natto. In recent years, direct genetic manipulation has been developed to facilitate more accurate and efficient improvements. However, the use of foreign DNA in these modifications has often faced public scrutiny and regulatory challenges. Bioengineer NISHIDA Keiji from Kobe University notes, “Due to stringent regulations and a lack of public acceptance, employing transgenic methods is often viewed unfavorably for food products.”
Nishida and his team have introduced a method that allows for more precise genetic alterations in microorganisms without relying on foreign DNA. He explains, “We have developed a DNA base editing technology called ‘Target-AID,’ which surpasses traditional techniques like ‘CRISPR-Cas9’ in various respects. Unlike CRISPR-Cas9, which can cause DNA breaks and cell death, Target-AID achieves precise point mutations without creating such breaks.”
In the journal Applied Microbiology and Biotechnology, the research team reports their collaboration with Bio Palette Co. Ltd. to apply this technique to important Lactobacillus strains used in dairy and pickle production. “We have edited specific locations in the genome with nearly 100% efficiency across two significantly different Lactobacillus species, indicating the technique’s versatility across various strains,” notes Nishida.
To demonstrate the potential of their method, they focused on a gene associated with the production of a compound that exacerbates type 2 diabetes. By applying Target-AID to mutate this gene, they engineered a Lactobacillus strain that can produce yogurt with significantly lower levels of this harmful chemical, making it safer for individuals with type 2 diabetes. Nishida remarks, “The bacteria we created do not fall under the regulations for genetically modified organisms when used as food, supplements, or medicines, and we anticipate that they can be easily commercialized following appropriate safety assessments.”
The research team also reported the capability to modify multiple genes simultaneously, highlighting their technique as a valuable tool for fundamental research. Looking ahead, Nishida envisions broad applications, stating, “We believe our findings will pave the way for probiotic products offering various health benefits, such as alleviating the impacts of lifestyle-related diseases, enhancing immunity, and improving allergic responses.”
This research was supported by the Japan Science and Technology Agency (grants JPMJOP1851 and JPMJGX23B4), the New Energy and Industrial Technology Development Organization, and the Japan Agency for Medical Research and Development (grants 21ek0109448h0002 and 24bk0104169s0201). It involved collaboration with researchers from Bio Palette Co. Ltd.
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