The coronavirus pandemic has bound the world to viruses like no other in memory, but new evidence shows that humans never even notice the great extent of viral existence – not even within ourselves.
A new database project compiled by scientists has identified more than 140,000 virus species that live in the human gut – a giant catalog that is all the more beautiful as more than half of these viruses were previously unknown to science .
When tens of thousands of newly discovered viruses sound like a disturbing development, it is completely understandable. But we should not misinterpret what these viruses actually represent in us, say researchers.
“It is important to remember that not all viruses are harmful, but are an integral part of the gut ecosystem,” explains biochemist Alexandre Almeida of the Bioinformatics Institute (EMBL-EBI) of the European Molecular Biology Laboratory and the Wellcome Sanger Institute.
“These samples come mainly from healthy individuals who have not had any specific diseases.”
The new virus catalog – called the Gut Phage Database (GPD) – has been complied with by analyzing more than 28,000 individual metagenomes – publicly available records of DNA sequencing of gut microbiome samples collected from 28 countries – along with nearly 2,900 reference genomes of cultured gut bacteria .
The results revealed that 142,809 virus species living in the human gut form a specific type of virus, known as a bacteriophage, which infects bacteria in addition to unicellular organisms called archaea.
In the mysterious environment of the gut microbiome – inhabited by a diverse mix of microscopic organisms, which include both bacteria and viruses – bacteriophages are thought to play an important role in regulating both bacteria and the health of the human gut itself. .
“Bacteriophages … deeply influence microbial communities by functioning as vectors of horizontal gene transfer, encoding additional functions beneficial to bacterial species, and promoting dynamic co-evolution interactions,” the researchers write in their new article .
Our knowledge of this phenomenon has long been stopped by limitations in our understanding of bacteriophage species.
In recent years, new advances in metagenomic analyzes have significantly expanded our awareness of the viral variety we are looking at here – and perhaps no more so than the Gut Phage Database, which researchers describe as a “massive expansion of human gut bacteriophage diversity” “.
“To our knowledge, this set represents the most comprehensive and complete collection of human gut phage genomes to date,” the study’s authors write.
“With an extensive database of high-quality phage genomes, the way is paved for a multitude of analyzes of the human gut virus with a much improved resolution, enabling the association of specific viral clades with clear microbiome phenotypes.”
The database updates everything we know about viral behavior.
The research shows that more than one third (36 percent) of identified viral clusters are not limited to the infestation of a single species of bacteria, meaning that they can create gene flow networks across phylogenetically distinct bacterial species.
In addition, the researchers found that 280 globally distributed viral clusters, including one newly identified clade, called Gubaphage, appear to be the second most common viral clot in the human gut, after the introduction of the crAssphage group.
In view of certain similarities between the two, the researchers initially thought that the Gubaphage might belong to a proposed family of crAssphage-like viruses, before establishing that the clades were actually distinct.
There is still so much to learn, and not just on the Gubaphage – but about more multitudes of viruses than we have ever dared to dream of. Thanks to these research efforts, tomorrow’s discoveries are closer and new insights will come faster.
“Bacteriophage research is currently experiencing a renaissance,” says microbiologist Trevor Lawley of the Wellcome Sanger Institute.
“This large-scale catalog of human gut viruses is at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future viral studies.”
The findings are presented in Cell.