The coronavirus pandemic has set the world on viruses as there is no time in living memory, but new evidence reveals that humans do not even notice the great 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 even more impressive given that more than half of these viruses were unknown to science.
If tens of thousands of newly discovered viruses sound like an alarming development, this is completely understandable. But we should not misinterpret what these viruses really represent within us, the researchers say.
“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 of the Institute of Bioinformatics of the European Molecular Biology Laboratory (EMBL-EBI) and Wellcome Sanger Institute.
“These samples came primarily from healthy individuals who did 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, publicly available DNA sequencing records of intestinal microbiome samples collected from 28 countries, along with nearly 2,900 reference genomes from cultured intestinal bacteria.
The results revealed 142,809 viral species residing in the human gut, constituting a specific type of virus known as bacteriophage, which infects bacteria, in addition to unicellular organisms called archaea.
In the mysterious environment of the intestinal 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 itself.
“Bacteriophages … profoundly influence microbial communities by functioning as horizontal gene transfer vectors, encoding ancillary beneficial functions for host bacterial species, and promoting dynamic coevolution 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 expanded our awareness of the viral variety we are examining here, and perhaps nothing more than the database of intestinal phages, which researchers describe as a “massive expansion of the diversity of bacteriophages in the human gut. “
“To our knowledge, this set represents the most complete and comprehensive collection of human intestinal phage genomes to date,” the study authors write.
“Having a complete database of high-quality phage genomes paves the way for a multitude of human gut viroma analyzes with much improved resolution, allowing the association of specific viral clades with phenotypes of different microbiomes “.
The database already updates what we know about viral behavior.
Research shows that more than a third (36%) of identified viral clusters are not limited to infecting a single species of bacteria, meaning they can create gene flow networks through phylogenetically different bacterial species.
In addition, researchers found 280 viral clusters distributed worldwide, including a newly identified clade, called Gubaphage, which appears to be the second most prevalent virus clade in the human gut, following what is known as the crAssphage group.
Given certain similarities between the two, the researchers initially thought that the Gubaphage might belong to a proposed family of crAssphage-like viruses, before determining that the clats were, in fact, different.
There is still much to learn, and not just in Gubaphage, but about more multitude of viruses than we have ever dared to dream of. Thanks to these research efforts, however, tomorrow’s discoveries are closer and new ideas will come more quickly.
“Research on bacteriophages is currently experiencing a renaissance,” says microbiologist Trevor Lawley of the Wellcome Sanger Institute.
“This large-scale, high-quality catalog of human gut viruses arrives at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies.”
The findings are reported in Cell.