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Scientists discover more than 140,000 unknown species of viruses in the human intestine

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A new trial with 28,000 microbiome samples from around the world offers data to investigate how these microorganisms that live in the gut affect health.

While the world continues to live under the ‘umbrella’ of masks and social distancing until the population is immunized with the vaccine, a surprising and invisible reality continues to emerge thanks to the continuous study of scientists: the identification and quantification of the microorganisms that live inside us, in our microbiome.

It shelters the invisible and until now most of them the great feared, especially with the invasion of SARS-CoV-2, microbes (bacteria, viruses, fungi and protozoa), which are actually the true ‘masters of the Earth’, but which also inhabit inside and on the surface of our body and whose role is key to the healthy development of our lives.

Inside of us

The microbiota is home to up to 100 billion of them. Science states that it has the potential to determine the health and disease of each individual, especially in the field of immunology. The microbiota weighs between 1.5 and 2 kilos, and accounts for 99% of all microorganisms residing in the human body. All of them include at least 1,000 different species of bacteria comprising more than 3 million genes (150 times more than in the human genome).

But we know a little more about it every day, and today we are surprised by a new study of ‘Cell’ carried out by researchers from the Wellcome Trust Sanger Institute and the European Institute of Bioinformatics, who have identified more than 140,000 viral species living in the human intestine, more than half of which have never been seen before.

With samples from around the world

The paper contains an analysis of more than 28,000 gut microbiome samples collected in different parts of the world. The amount and diversity of viruses found by researchers was surprisingly high, and the data opens up new avenues of research to understand how they affect human health from ‘our own guts’.

The human gut is an environment with incredible biodiversity. In addition to bacteria, hundreds of thousands of viruses called bacteriophages also live there and can infect them.

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

Metagenomics

Using a DNA sequencing method called metagenomics, researchers explored and catalogued the biodiversity of viral species found in 28,060 human intestinal metagenomas and 2,898 isolated bacterial genomes, grown from the human gut.

Dr Alexandre Almeida, co-author of the trial, says: “It is important to remember that not all viruses are harmful, but they represent an integral component of the intestinal ecosystem. On the one hand, most of the viruses we find have DNA as genetic material, which is different from the pathogens most people know, such as SARS-CoV-2 or Zika, which are RNA viruses. Second, these samples come mainly from healthy people who do not share any specific disease. It’s fascinating to see how many unknown species live in our gut and try to unravel the bond between them and human health.”

Among the tens of thousands of viruses discovered, a new, highly prevalent one was identified, a group of viruses believed to have a common ancestor, which the authors refer to as Gubaphage. This was found to be the second most prevalent group of viruses in the human gut, after crAssphage, which was discovered in 2014.

Both viruses appear to infect similar types of human gut bacteria, but without further research, it is difficult to know the exact functions of the newly found Gubaphage.

The future

Speaking to media, Dr Luis F. Camarillo-Guerrero, first author of the study, clarifies to readers: “An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality. The strict control of the same during the process together with a machine learning approach allowed us to mitigate the contamination and thus obtain very complete them. High-quality viral genomes pave the way to better understand the role that viruses play in our gut microbiome, including the discovery of new treatments such as antimicrobials of bacteriophage origin.”

And he insists: “In this work, we generate the most complete database of bacteriophage genomes (or phages for short) of the human intestine, which houses more than 142,000 genomes, and which we call the Gut Phage Database (or GPD, These genomes are derived, as mentioned above, from 28,060 human metagenomic samples. Importantly, these samples span 6 continents and 28 countries, allowing us to largely capture the diversity of human phages. intestines around the world. For example, 280 phages were detected on at least 5 continents and we also found that phages from rural communities. They tend to differ from those found in urban settings. In particular, more than half of the phages we discovered were new (> 70,000 species), which significantly sheds light on the diversity of bacterial viruses that inhabit the human gut.”

Research co-author Dr Trevor Lawley said: “The bacteriophage study is undergoing a renaissance. This high-quality, large-scale catalog of human intestinal viruses comes at the right time to serve as a model to guide ecological analysis and evolutionary in future virome studies”.

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