New human gut virus found hidden in plain sight

Whereas the microbiome, the bacteria in our gut, is being extensively characterized, the bacteriophages that live with them remain a mystery. Studies of the gut viral metagenome have labelled most of its sequences 'unknown', because they bear little resemblance to those in databases. 

In a study appearing in Nature Communications¹, researchers used a novel technique to investigate the unknown fraction and discovered a new virus shared across most human microbiome samples.

“When it comes to viruses, even those within our body remain unknown,” says Ramy Aziz of Cairo University, one of the authors of the study. To piece together these unknown viruses, the researchers searched published viral metagenome data of faecal samples from 12 people to find sequences which co-varied across them. Such sequences are likely to be from the same bacteriophage and could be used to reassemble its genome. 

“We show that among these unknown sequences there is at least one example of a highly abundant bacteriophage that is shared by many people. This means that the intestinal virome is not as unique to an individual as previously thought,” says Bas Dutilh, lead author of the study. 

The new virus, dubbed crAssphage, is six times more abundant than all known virome bacteriophages combined. Most of the proteins encoded by crAssphage's genome don't match known sequences, leaving its precise biology a mystery for future research. “crAssphage is an example of a virus which is so unknown that scientists failed to identify it even though it's ubiquitous,” adds Aziz.

In addition to discovering crAssphage, this work creates the possibility of characterizing the similarities between people's gut viromes in the same manner as the microbiome has been classified into enterotypes.

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