The coronavirus pandemic has left the world fixated on viruses like never before, but new evidence shows that people don’t even notice the enormity of viral existence, even when it’s inside us.
A new database project curated by scientists has identified more than 140,000 viral species living in the human gut – a gigantic catalog that is all the more amazing considering more than half of these viruses were previously unknown to science.
If tens of thousands of newly discovered viruses sounds like an alarming development, that is completely understandable. But we shouldn’t misinterpret what these viruses in us actually represent, researchers say.
“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 were mainly from healthy individuals who did not have specific diseases.”
The new virus catalog – the Gut Phage Database (GPD) – was adhered to 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 numbers of cultured gut bacteria.
The results revealed 142,809 viral species that live in the human gut and produce 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, including both bacteria and viruses – bacteriophages are believed to play an important role in regulating bacteria as well as the health of the human gut itself.
“Bacteriophages … profoundly impact microbial communities by functioning as vectors of horizontal gene transfer, encoding additional functions beneficial to host bacterial species, and by promoting dynamic co-evolutionary interactions,” the researchers write in their new paper.
Our knowledge of this phenomenon has long been delayed by limitations in our understanding of bacteriophage species.
In recent years, new advancements in metagenomic analyzes have significantly increased our awareness of the viral variety we are looking at here – and perhaps no more so than the Gut Phage Database, which the researchers describe as “ a massive expansion of the diversity of human gut bacteriophages. ” “.
“To our knowledge, this set represents the most comprehensive and complete collection of human gut phage genomes to date,” write the study authors.
“Having an extensive database of high quality phage genomes paves the way for a multitude of analyzes of the human gut viroma with greatly improved resolution, allowing for the association of specific viral clades with different microbiome phenotypes.”
The database is already updating what we know about viral behavior.
The research shows that more than a third (36 percent) of the identified viral clusters are not limited to infecting a single bacterial species, meaning they can create gene flow networks across phylogenetically distinct bacterial species.
In addition, the researchers found 280 viral clusters distributed worldwide, including a newly identified clade called Gubaphage, which appears to be the second most common viral clade in the human gut, after what is known as the crAssphage group.
Given certain similarities between the two, the researchers initially thought the Gubaphage might belong to a proposed family of crAssphage-like viruses, before determining that the clades were, in fact, different.
There is still so much to learn, and not just about the Gubaphage – but about more masses of viruses than we could ever have imagined. However, thanks to these kinds of research efforts, tomorrow’s discoveries are closer and new insights will come faster.
“Bacteriophage research is currently experiencing a renaissance,” said microbiologist Trevor Lawley of the Wellcome Sanger Institute.
“This high-quality, large-scale catalog of human gut viruses is timely to serve as a blueprint for ecological and evolutionary analysis in future virome studies.”
The findings are reported in Cell