Using CRISPR to Alter the Microbiome

Researchers at Western University have developed a new method to deliver the DNA-editing tool CRISPR-Cas9 into microorganisms in the lab, making it possible to efficiently launch a targeted attack on specific bacteria. The study, published today in Nature Communications, opens up the possibility of using CRISPR to alter the makeup of the human microbiome in a way that could be specific from person to person. It also presents a potential alternative to traditional antibiotics to kill bacteria like S.aureus or E.coli.

“One of the major reasons that I am excited about this work is that it has a wide range of possible real-world applications,” says coauthor Bogumil Karas. “It has the potential for development of next generation antimicrobial agents that would be effective even for bacteria that are resistant to all known antibiotics. This technology could also be used to help ‘good’ bacteria produce compounds to treat diseases caused by protein deficiencies.”

CRISPR and can be programmed to target and edit DNA at precise locations. Researchers use CRISPR to permanently modify genes in living cells and organisms. In the same way, CRISPR can be programmed to kill bacteria—but, until now, there wasn’t a way to efficiently and specifically target certain bacterial strains.

“Using CRISPR to kill things isn’t a new idea because that’s what CRISPR does naturally," says senior author David Edgell. “The problem has always been how you get CRISPR to where you want it to go. Other delivery systems could only go to a few spots, where ours can go anywhere.”

The delivery system developed at Western uses bacteria’s natural ability to replicate—called bacterial conjugation—to deliver CRISPR to specific bacteria in order to alter its DNA and kill it.