Publication Bas Dutilh in Nature Communications

Dutilh, Bas

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.

Odds are, there's a virus living inside your gut that has gone undetected by scientists for hundreds, and possibly hundreds of thousands, of years. A new study led by researchers at Radboudumc and San Diego State University, California, has found that approximately half the world's population is host to a newly described virus, named crAssphage. The research appears today in Nature Communications.

Dr. Bas E. Dutilh, a bioinformatician at the Centre for Molecular and Biomolecular Informatics at Radboudumc and lead author on the publication, and his colleagues at San Diego State University, stumbled upon the discovery quite by accident. They used the results of previous studies into the viruses inhabiting the human gut to screen for viruses shared by many people. In the viral DNA isolated from fecal samples from twelve different individuals, they noticed a particular sequence that all the samples had in common, but was completely unlike any previously known virus. After further assembly of the DNA sequences, they obtained a genome of 97,065 nucleotides long, which is ten times the size of the HIV genome. Some of the proteins encoded on the genome are similar to those found in other well-described viruses. This allowed Dutilh's team to determine that their novel virus is one known as a bacteriophage, which infects and replicates inside bacteria. They named the virus crAssphage, after the software program used to discover it. Using additional innovative bioinformatic techniques, they predicted that this particular bacteriophage proliferates by infecting a common gut bacterium known as Bacteriodetes.

The researchers then screened for the virus across the databases of the National Institute of Health's Human Microbiome Project (HMP), and Argonne National Laboratory's MG-RAST database, and found it in high abundance in samples derived from human feces. It turned out, that this was a new virus that about half the sampled people had in their bodies, but that nobody knew about.

"It's exceptional to find a virus shared by so many people," Dutilh said. "Until now, we thought that the viruses in our gut are highly specific to an individual, but these results show that the contrary can be true: viruses exist that are highly conserved between totally unrelated people. What is more, based on the available DNA sequencing information from fecal samples around the world, crAssphage is over six times more abundant than all the previously known bacteriophages put together." Further details about crAssphage have been difficult to come by. The makeup of the viral genome suggests that it's circular in structure.

Further laboratory work has confirmed that the viral DNA is a singular entity, but it's proven difficult to isolate. It's unknown how the virus is transmitted, but given the fact that it is so widespread and abundant, it is tempting to speculate that it might be a good candidate for personalized manipulation of the gut flora for the treatment of intestinal diseases. When Dutilh presented his results at a scientific conference in Zürich last week, bacteriophage researchers were interested in isolating and further characterizing crAssphage in the near future.

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.
Bas E. Dutilh, Noriko Cassman, Katelyn McNair, Savannah E. Sanchez, Genivaldo G. Z.Silva, Lance Boling, Jeremy J. Barr, Daan R. Speth, Victor Seguritan, Ramy K.Aziz, Ben Felts, Elizabeth A. Dinsdale, John L. Mokili, Robert A. Edwards.
Nature Communications, 5: 4498, 24 July 2014.


Other links related to this article: 

- National Geographic Not Exactly Rocket Science 
- NPR Goats and Soda 
- NPR Science Friday (radio interview Rob Edwards) 
- New Scientist
- Der Spiegel 
- Die Welt 




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