• High diversity
• A new virus
What is already known on this topic
The human gut is home not only to trillions of bacteria, but also to the viruses, called bacteriophages, that infect those bacteria. However, little is known about the number and the diversity of bacteriophages in the gut.What this research adds
By analyzing more than 28,000 gut microbiome samples collected in different parts of the world, researchers have found about 142,000 viral species living in the human gut, most of which had never been identified before. The number and diversity of the viruses were surprisingly high, the researchers found. Among the new-found gut viruses, the researchers identified a highly prevalent clade — a group of viruses that is thought to have a common ancestor — that they called the Gut Bacteroidales phage, or Gubaphage. The newly discovered Gubaphage is the second most prevalent virus clade in the human gut.Conclusion
The findings could facilitate future studies aimed at understanding how gut bacteriophages affect human health.
The human gut is home not only to trillions of bacteria, but also to the viruses, called bacteriophages, that infect those bacteria. Now, researchers have found more than 140,000 viral species living in the human gut, most of which had never been identified before.
The findings, published in Cell, could facilitate future studies aimed at understanding how gut bacteriophages affect human health. “It’s important to remember that not all viruses are harmful, but represent an integral component of the gut ecosystem,” says study co-author Alexandre Almeida at the EMBL-EBI and the Wellcome Sanger Institute.
To assess the number and the diversity of bacteriophages in the human gut, Almeida and his colleagues, led by Luis Camarillo-Guerrero and Trevor Lawley at the Wellcome Sanger Institute, sequenced and analyzed the genomes contained in more than 28,000 gut microbiome samples.
High diversity
The number and diversity of the viruses in the human gut were unexpectedly high, the researchers found. The team identified about 142,000 viral species, of which 80% could not be assigned to a known viral family. The rest mostly belonged to the Podoviridae, Siphoviridae, and Myoviridae viral families, which were previously reported to be enriched in human feces.
When the researchers measured the bacteriophage diversity within four common human gut bacteria — Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteriota — they found that Firmicutes harbor a significantly higher viral diversity than the other types of bacteria.
Further experiments showed that about one third of gut bacteriophages infect several different bacteria rather than a single bacterial species. The team also created a database dubbed the Gut Phage Database, which contains the tens of thousands of viruses discovered.
A new virus
Among the new-found gut viruses, the researchers identified a highly prevalent clade — a group of viruses that is thought to have a common ancestor — that they called the Gut Bacteroidales phage, or Gubaphage. The newly discovered Gubaphage is the second most prevalent virus clade in the human gut, after the previously described crAssphage, the team found.
Although crAssphage and Gubaphage viruses appear to infect similar types of gut bacteria, it’s unclear what the exact functions of the Gubaphage are.
“Bacteriophage research is currently experiencing a renaissance. 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,” Lawley says.
Almeida notes that the gut microbiome samples were mostly collected from healthy people. “It’s fascinating to see how many unknown species live in our gut, and to try and unravel the link between them and human health,” he says.
