Newly Discovered Gut Virus Is In At Least Half of All Humans

Schematic representation of the circular crAssphage genome / B.E. Dutilh et al., Nature Communications 2014
Janet Fang 25 Jul 2014, 02:36

Scientists have discovered a virus that lives in the gut of more than half -- maybe even 75 percent -- of the world’s population. But it probably won’t make you sick. The virus infects and replicates itself inside one of the most common types of gut bacteria, Bacteroidetes, which has been implicated in obesity, diabetes, and other gut-related diseases. 

They call it crAssphage, and it’s described in Nature Communications this week. 

This newly discovered bacteria-infecting virus (or bacteriophage) was stumbled on by accident. Bas Dutilh and Robert Edwards from San Diego State University were screening for new viruses, analyzing the DNA in fecal samples from 12 people. That's when they noticed how all the samples had a particular cluster of viral DNA about 97,000 base pairs long -- that’s about 10 times as big as HIV. They found nothing like it among known viruses. 

When they screened for the virus in national, publicly available databases, they found that it was “highly abundant” in human feces-derived samples. Then, using DNA amplification, the team located the virus in the original samples to validate that the viral DNA they found on their computer actually exists in real life. 

It turned out to be a new virus that the majority of people sampled had in their bodies that nobody knew anything about. It was present in 342 of the 466 fecal “metagenomes” they looked at. So if crAssphage isn't in you, you'll likely find it in the person next to you. “It’s not unusual to go looking for a novel virus and find one,” Edwards says in a news release. “But it’s very unusual to find one that so many people have in common. The fact that it’s flown under the radar for so long is very strange.”

They named it after the cross-assembly software program used for its discovery -- and not after where the virus is found. "Oh, no, we never thought of that," Edwards tells NPR. "We would never be crass."

Since some of crAssphage’s proteins are like those found in well-known viruses, Dutilh and colleagues were able to figure out that it’s a bacteriophage, and they further predict that it proliferates by infecting the common gut bacteria Bacteriodetes, which live toward the end of the intestinal tract.

Because it’s so widespread, it can’t be very young -- probably as old as humans are. So how is it that we’ve only just detected this super common virus that’s inside at least half of us? Shrug... but it happens a lot. According to Dutilh, three-fourths of the DNA sequences in a new stool sample are unknown. 

Further details about crAssphage have been hard to come by. “We know it’s there, but we can’t capture it quite yet,” Edwards says. They do know that it’s not found in very young infant fecal samples, so it’s not acquired from the mom. Also, the makeup of the viral DNA suggests it has a circular structure (pictured). 

Once it’s isolated, the researchers hope to explore the virus’s role in obesity. If crAssphage mediates the activity of Bacteriodetes colonies, it might have a hand in promoting or suppressing obesity-related processes. 

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