Scientists find 140,000 species of viruses in the human gut, and most are unknown

The coronavirus pandemic has made the world obsessed with viruses like no other time in living memory, but new evidence reveals that humans do not even notice the vast extent of viral existence, even when it is within us.

A new database project compiled by scientists has identified more than 140,000 viral species that inhabit the human gut, a giant catalog that is all the more surprising given that half of these viruses were previously unknown to science.

If tens of thousands of newly discovered viruses sounds like an alarming development, that’s completely understandable. But we must not misunderstand what these viruses actually represent within us, say the researchers.

“It is important to remember that not all viruses are harmful, but they represent an integral component of the intestinal ecosystem,” explains biochemist Alexandre Almeida from the Bioinformatics Institute of the European Molecular Biology Laboratory (EMBL-EBI) and the Wellcome Sanger Institute.

“These samples come mainly from healthy people who do not share any specific disease.”

The new virus catalog, called the Gut Phage Database (GPD), was completed by analyzing more than 28,000 individual metagenomes, DNA sequencing records of gut microbiome samples collected from 28 countries, along with nearly 2,900 genomes from reference of cultured intestinal bacteria.

The results revealed 142,809 viral species that reside in the human intestine, constituting a specific type of virus known as a bacteriophage, which infects bacteria, in addition to single-celled organisms called archaea.

In the mysterious environment of the gut microbiome, inhabited by a diverse mix of microscopic organisms, encompassing both bacteria and viruses, bacteriophages are believed to play an important role, regulating both bacteria and the health of the human gut.

“Bacteriophages … profoundly influence microbial communities by functioning as horizontal gene transfer vectors, encoding beneficial accessory functions for bacterial host species, and promoting dynamic coevolutionary interactions,” the researchers write in their new paper.

For a long time, our knowledge of this phenomenon was stalled by limitations in our understanding of bacteriophage species.

In recent years, new advances in metagenomic analysis have significantly broadened our understanding of the viral variety we are seeing here, and perhaps none more than the Gut Phage Database, which researchers describe as a “massive expansion of the diversity of human intestinal bacteriophages “. “.

“To our knowledge, this set represents the most complete and comprehensive collection of human gut phage genomes to date,” the study authors write.

“Having a comprehensive database of high-quality phage genomes paves the way for a multitude of analyzes of the human gut virome with greatly improved resolution, allowing the association of specific viral clades with distinct microbiome phenotypes.”

The database is already updating what we know about viral behavior.

Research shows that more than a third (36 percent) of the identified viral groups are not restricted to infecting a single species of bacteria, meaning that they can create networks of gene flow across phylogenetically distinct bacterial species.

Furthermore, the researchers found 280 globally distributed viral groups, including a recently identified clade, called Gubaphage, which appears to be the second most prevalent virus clade in the human gut, after what is known as the crAssphage group.

Given certain similarities between the two, the researchers initially thought that Gubaphage might belong to a proposed family of viruses similar to crAssphage, before determining that the clades were, in fact, distinct.

There is still a lot to learn, and not just about Gubaphage, but about more viruses than we ever dared dream of. However, thanks to research efforts like this, the discoveries of tomorrow are closer and new knowledge will come faster.

“Bacteriophage research is undergoing a renaissance,” says microbiologist Trevor Lawley of the Wellcome Sanger Institute.

“This large-scale, high-quality catalog of human intestinal viruses comes at the right time to serve as a model to guide ecological and evolutionary analysis in future virome studies.”

Findings are reported in Cell.


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