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Thousands of new gut virus species identified

Friday February 19th 2021

More than 140,000 virus species that live in the human gut have been identified – more than half of which are new to science, a new study revealed last night.

Among the tens of thousands discovered, a new highly prevalent clade – a group of viruses believed to have a common ancestor – was identified, which the researchers at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) refer to as the Gubaphage.

This was found to be the second most prevalent virus clade in the human gut, after the crAssphage, which was discovered in 2014.

Both of these viruses appear to infect similar types of human gut bacteria, but it is not yet known what the functions of the newly discovered Gubaphage are.

The paper, published yesterday in Cell, analyses more than 28,000 gut microbiome samples collected in different parts of the world.

Although it is known that gut microbiome imbalances can contribute to diseases and complex conditions such as inflammatory bowel disease, allergies and obesity, little is known about the role our gut bacteria, and the bacteriophages that infect them, play in human health and disease.

Using metagenomics, the research team catalogued the biodiversity of the viral species found in 28,060 public human gut metagenomes and 2,898 bacterial isolate genomes cultured from the human gut.

They identified more than 140,000 viral species living, more than half of which have never been seen before.

First author Dr Luis F Camarillo-Guerrero, of the Wellcome Sanger Institute, said: “An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality. A stringent quality control pipeline coupled with a machine learning approach enabled us to mitigate contamination and obtain highly complete viral genomes.

“High-quality viral genomes pave the way to better understand what role viruses play in our gut microbiome, including the discovery of new treatments such as antimicrobials from bacteriophage origin.”

The results of the study form the basis of the Gut Phage Database (GPD), a database containing 142,809 non-redundant phage genomes. It will be an “invaluable” resource for those studying bacteriophages and the role they play on regulating the health of gut bacteria, the researchers say.

Senior study author Dr Trevor Lawley, from the Wellcome Sanger Institute, added: “This high-quality, large-scale catalogue of human gut viruses comes at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies.”

Camarillo-Guerrero LF et al. Massive expansion of human gut bacteriophage diversity. Cell 18 February 2021

[abstract]

Tags: Europe | Flu & Viruses | Gastroenterology | UK News

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