CRISPR Used to Eliminate Harmful Bacteria in the Gut Microbiome

CRISPR Used to Eliminate Harmful Bacteria in the Gut Microbiome

A team of researchers at North Carolina State University have used the CRISPR-Cas3 gene editing system to target harmful bacteria in the gut microbiome that cause colitis, a form of inflammatory bowel disease.

Colitis has many different causes, one of which is Clostridioides difficile bacteria in the gut. C. difficile is responsible for almost all cases of pseudomembranous colitis and between 10% and 25% of antibiotic-associated diarrhea. Treatment with antibiotics can upset the normal balance of bacteria in the gut that keeps C. difficile in check and stops the bacteria from multiplying and causing colitis.

Antibiotics can be used to treat C. difficile; however, while the antibiotics kill C. difficile they can also wipe out good bacteria and relapse occurs in around 30% of patients.

Bacteriophages infect bacteria and hijack their cellular machinery to create new bacteriophages. They then burst out of the bacteria killing it in the process. Bacteriophages do not usually harm humans, so they have potential to be used in treatments for bacterial infections. The NC researchers teamed up with Locus Biosciences in a proof-of-concept study to determine if a programable CRISPR could be delivered by bacteriophages to specifically target C. difficile in the gut.

“We wanted to engineer phages with self-targeting CRISPR payloads and deliver them to the gut of an organism of choice—in this case a mouse—in order to have a beneficial impact on host health and to prevent disease,” explained Rodolphe Barrangou, co-corresponding author of a paper.

CRISPR-Cas3 was programmed to specifically target C. difficile and cause massive damage to the DNA to kill the bacteria, without affecting other types of bacteria in the gut microbiome. The researchers tested the CRISPR-Cas3-delivering phages in the lab and showed they were effective at selectively killing C. difficile bacteria. They then switched to live animal studies. After introducing the phages, C. difficile levels in the gut were reduced, but there was relapse after two days and the C. difficile bacteria returned to pre-treatment levels.

While the study was not a total success, the researchers did demonstrate that CRIPR-carrying phages can be used to selectively kill gut bacteria. “This was a positive first step in a long process,” said Barrangou.

The researchers are now refining their techniques and are re-tooling the phages to prevent relapse after the first round of killing.  The researchers are also developing a range of different phages to target other strains of C. difficile.

You can read more about the study in the paper – In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials – which was recently published in the journal mBio. DOI: 10.1128/mBio.00019-20

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