Global collaboration of scientists uncovers human microbiome virus in one-third of all countries

Publication Utrecht scientists in Nature Microbiology

We are all the same, yet we are all different. New research from bioinformatician Bas Dutilh at Utrecht University has shown how a family of tiny viruses lives the guts of humans around the world, yet changes depending on which country we are from.

The crAssphage-virus. Credit: Colin Hill

In a global collaboration with more than 100 scientists drawn from 65 countries, the team analysed sewage and faecal samples. In a publication in Nature Microbiology on 8 July, they describe that the virus crAssphage can be found in one-third of the countries of the world.


CrAssphage is a common virus that can be found in the human gut. It is a bacteriophage that infects bacteria. In 2014, Bas Dutilh discovered crAssphage by serendipity. “We were analysing large-scale data using our new tool, cross-assembly (crAss), and found this bacteriophage. We called it crAssphage, after the computational tool”, says senior author Bas Dutilh. “It was surprising that so far scientists had overlooked it. Once we knew what we were looking for, we could find the genome in lots of samples. By the time we published the paper describing that work, we had looked at all publicly available metagenomes — 2,944 at that time – and found crAssphage in 73 percent of the human faecal metagenomes that were then publicly available.”

The project turned out to be bigger and more collaborative than we could have imagined

CrAssphage became world news. By now more than 300 papers have been published about the new-found virus. “Several questions repeatedly rose from the people we talked to. Where does it come from? And, is there any evidence that it affects either the health or disease status of humans? To answer these questions, we decided to call in the help of scientists worldwide. We sent an email to our friends and colleagues, and tweeted about our quest. The project turned out to be bigger and more collaborative than we could have imagined. Scientists worldwide devoted their time and effort to join our hunt for crAssphage.”


This new research shows why crAssphage is so widespread. In the paper, the team provides evidence that crAssphage has been with us since the dawn of humankind. They show that it is not associated with human disease, providing an explanation as to why it has not been removed from the population. “We found closely related viruses in faecal samples from gorillas, monkeys, and other wild primates. Based on these results, we think that it has evolved with us for millions of years, and spread with humans across the globe", says Dutilh. "This is the first time anyone has shown that human gut viruses can be at least as old as the human lineage.”

Because the virus is so common among humans, crAssphage is now a powerful indicator of faecal pollution and human impacts on the environment. One day the virus may help scientists manipulate the gut microbiome by targeting harmful bacteria.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage was published on 8 July in Nature Microbiology. DOI: 10.1038/s41564-019-0494-6.