bacteriophage
Bacteriophage illustration, Image Credit: medicalnewstoday

Viruses are the most biological entities on earth. Presently scientists at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) have identified over 140,000 viral species living in the human gut, more than half of which are new to science.

The study published on 18 February 2021 in Cell, contains an analysis of over 28,000 gut microbiome samples collected in various parts of the world.

The number & diversity of the viruses the scientists discovered were shockingly high, and the data opens up new research doors for understanding how viruses living in the gut affect human health.

The human gut is an incredibly biodiverse environment. In addition to bacteria, a huge number of infections of viruses called bacteriophages, which can infect bacteria, likewise live there.

It is realized that imbalances in our gut microbiome can contribute to diseases and complex conditions like — Inflammatory Bowel Disease, allergies, and obesity. But relatively little is thought about the role our gut bacteria, and the bacteriophages that infect them, play in human wellbeing and disease.

Utilizing a DNA-sequencing technique called metagenomics*, scientists at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) explored and cataloged the biodiversity of the viral species discovered in 28,060 public human gut metagenomes and 2,898 bacterial isolate genomes refined from the human gut.

The analysis found over 140,000 viral species living in the human gut, more than half of which have never been seen.

 Dr. Alexandre Almeida, Postdoctoral Fellow at EMBL-EBI and the Wellcome Sanger Institute said that “It’s important to remember 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 people know, such as 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 see how many unknown species live in our gut, and to try and unravel the link between them and human health.”

Among the huge number of viruses found, another highly prevalent clade – or group of viruses believed to have a common ancestor – was identified, which the authors refer to as the Gubaphage.

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

Both of these viruses appear to infect similar types of human gut bacteria, however, without further research, it’s very hard to know the exact functions of the newfound Gubaphage.

Dr. Luis F. Camarillo-Guerrero, the first author of the study from the Wellcome Sanger Institute, said that “An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality. Astringent 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 outcomes of the study form the basis of the Gut Phage Database (GPD), a highly curated database containing 142,809 non-excess phage genomes that will be an important resource for those considering bacteriophages and the role they play in regulating the health of both our gut bacteria & ourselves.

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

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