SDSU discovers gut virus related to obesity

by Michelle Monroy, Senior Staff Writer

There is a new gut virus that lives in half of the world population and was discovered by researchers at San Diego State.

The virus, which has gone undetected for decades, infects common gut bacteria that could be connected to obesity, diabetes and other related diseases.

Robert Edwards, associate professor of computer science, was the principal investigator of the study that found crAssphage, the name the virus was given. He was working with Bas E. Dutilh, who is the primary researcher of the study. The research paper has been published in Nature Communications.

CrAssphage was named after the special software program called crAss, or comparative metagenomics by cross-assembly, that helped identify this virus.

“It’s a virus that specifically attacks and kills a certain type of bacterium that is very common in human intestines,” dean of the College of Sciences Stanley Maloy said.

The virus is 97,000 base pairs long, which is about 10 times the amount of DNA base pairs in HIV.

The Research

The virus was found when researchers using the software program noticed some fragments that were common in many different samples.

“We were analyzing sequence data and we noticed that there were some fragments that were common in lots of different samples,” Edwards said.

He said that of the 499 samples they tested, the virus was present in about 75 percent.

After the virus was found through the computer software program, researchers asked biologists to confirm if what they had found using computers was present biologically.

John Mokili, a virologist at SDSU, developed a test that proved the newly discovered virus was present in the original fecal samples. The virus that Mokili found was nearly 100 percent identical to the virus Edwards’ lab had found.

“Generally it was close to 100 percent similarity to the DNA data that was found using the bioinformatic method, it was quite impressive,” Mokili said.

Unusual Method of Discovery

Mokili said this study is different because when discovering a virus, researchers usually begin by gathering samples from patients with a disease, then find a virus biologically and later pass on that information to bioinformatics researchers for further analysis.

“It’s unusual—normally it’s the other way around,” Edwards said. “Normally what happens is that the biologists generate some data and the computer science people analyze the data.”

Researchers are still not completely sure what the virus does but they do know the virus is associated with very common bacteria found in the gut called bacteroides.

Personalized Phage Medicine

“Bacteroides are very important in our health, it seems to be implicated in diabetes, irritable bowel syndrome and Crohn’s disease,” Edwards said.

Bacteroides are also suspected to play a role between gut bacteria and obesity.

“This virus may play a role in all of us whether we will become obese or not,” Maloy said.

In the future they hope to develop “personalized phage medicine,” which is a term coined on SDSU’s campus.

“The idea is that we would isolate phages from you, manipulate them and then feed them back to you,” Edwards said. “We can manipulate them in ways that can allow us to alter your bacterial community, so we can maybe prevent diabetes or reduce the likelihood that you would have diabetes.”

According to Edwards the next step in the research process is to find out more about the virus, isolate it and examine how it interacts with other bacteria.

“It’s most innovative, relying on real expertise of the faculty and students, here at SDSU and has potential impact on humankind,” Maloy said.

Edwards said the finding exemplifies SDSU’s continued efforts as a leading research school.

“It really demonstrates that SDSU is a world-class research institution that is at the forefront of very cutting edge research, that’s something we’re really proud of,” Edwards said.