Over 140,000 viral species living in the human gut

The paper, published today (18 February 2021) in Cell, contains an analysis of over 28,000 gut microbiome samples collected in several parts of the planet .

The amount and variety of the viruses the researchers found was surprisingly high, and therefore the data reveal new research avenues for understanding how viruses living within the gut affect human health.

The human gut is an incredibly biodiverse environment. additionally to bacteria, many thousands of viruses called bacteriophages, which may infect bacteria, also live there.

It is known that imbalances in our gut microbiome can contribute to diseases and sophisticated conditions like Inflammatory Bowel Disease, allergies and obesity.

But relatively little is understood about the role our gut bacteria, and therefore the bacteriophages that infect them, play in human health and disease.

Using a DNA-sequencing method called metagenomics, researchers at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) explored and catalogued the biodiversity of the viral species found in 28,060 public human gut metagenomes and a pair of,898 bacterial isolate genomes cultured from the human gut.

The analysis identified over 140,000 viral species living within the human gut, quite half which haven’t been seen before.

Dr Alexandre Almeida, Postdoctoral Fellow at EMBL-EBI and therefore the Wellcome Sanger Institute, said: “It’s important to recollect that not all viruses are harmful, but represent an integral component of the gut ecosystem. For one thing, most of the viruses we found have DNA as their genetic material, which is different from the pathogens most of the people know, like SARS-CoV-2 or Zika, which are RNA viruses. Secondly, these samples came mainly from healthy individuals who didn’t share any specific diseases. It’s fascinating to ascertain what percentage unknown species live in our gut, and to undertake and unravel the link between them and human health.”

Among the tens of thousands of viruses discovered, a replacement highly prevalent clade — a bunch of viruses believed to possess a standard ancestor — was identified, which the authors ask because the Gubaphage.

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

Both of those viruses seem to infect similar sorts of human gut bacteria, but without further research it’s difficult to understand the precise functions of the newly discovered Gubaphage.

Dr Luis F. Camarillo-Guerrero, first author of the study from the Wellcome Sanger Institute, said: “An important aspect of our work was to make sure that the reconstructed viral genomes were of the very best quality. A stringent internal control pipeline including a machine learning approach enabled us to mitigate contamination and acquire highly complete viral genomes. High-quality viral genomes pave the thanks to better understand what role viruses play in our gut microbiome, including the invention of latest treatments like antimicrobials from bacteriophage origin.”

The results of the study form the idea of the Gut Phage Database (GPD), a highly curated database containing 142,809 non-redundant phage genomes which will be a useful resource for those studying bacteriophages and therefore the role they play on regulating the health of both our gut bacteria and ourselves.

Dr Trevor Lawley, senior author of the study from the Wellcome Sanger Institute, said: “Bacteriophage research is currently experiencing a renaissance. This high-quality, large-scale catalogue of human gut viruses comes at the proper time to function a blueprint to guide ecological and evolutionary analysis in future virome studies.”

Source : Wellcome Trust Sanger Institute