Successfully edited genes of gut bacteria in living mice

A research team led by synthetic biologist Xavier Duportet, co-founder of biotech company Eligo Bioscience, has successfully designed a gene-editing tool that can modify the bacterial population in the gut microbiota of living mice.

Initial experiments showed that the tool modified the target gene in more than 90% of Escherichia coli colonies in the intestines of living mice. Escherichia coli is a type of bacteria that normally lives in the intestines of humans and animals. Most strains of E. coli are known to cause transient and mild diarrhea, but some strains of the bacteria are known to cause more serious intestinal infections with diarrhea, abdominal pain, and fever.

Some previous studies have used the CRISPR—Cas ​​gene-editing system to kill harmful bacteria in the guts of mice. But Duportet and colleagues wanted to edit the genes of bacteria in the gut microbiome without killing them.

To do this, scientists used a method that swaps one nucleotide base for another – such as converting an A to a G – without breaking the DNA double strand. Until now, most existing methods have failed to modify the target bacterial population sufficiently to be effective. This is because the vectors they introduce only target receptors that are commonly found in bacteria grown in the lab.

To overcome this obstacle, Duportet and his colleagues created a delivery vehicle that uses components of a bacteriophage—a virus that infects bacteria—to carry several E. coli receptors expressed in the gut environment. The vector carries a “basically gene-editing tool” that targets specific E. coli genes. The team also modified the system to prevent the delivered genetic material from replicating and spreading once inside the bacteria.

The team introduced the basic gene-editing tool into mice and used it to change an A to a G in an E. coli gene that produces β-lactamase — an enzyme that makes bacteria resistant to certain antibiotics. About eight hours after the animals were treated, about 93 percent of the target bacteria had their genes edited.

The researchers then tweaked the editing tool to modify E. coli genes that produce a protein thought to play a role in some neurodegenerative and autoimmune diseases. The percentage of bacteria that were edited hovered around 70 percent within three weeks of the mice being treated. In the lab, the scientists were also able to use the tool to edit strains of E. coli and Klebsiella pneumoniae that can cause pneumonia infections. This suggests that the editing system can be tweaked to target different strains and species of bacteria.

The achievement represents a “major leap” in developing tools that can modify bacteria directly inside the gut, opening up the possibility of fighting disease while also preventing harmful DNA from spreading.

The next step for Duportet and colleagues is to develop mouse models of microbiome-induced diseases to measure whether specific gene edits have beneficial effects on their health.