Over half of them have never been seen before. The number and variety of the viruses in the human gut were a big surprise for the researchers, who believe the finding will lead to new investigations to understand how these viruses affect human health.
You’re never alone. Our bodies are hosts to hundreds of thousands of bacteria, viruses, fungi, and parasites living (for the most part) in harmony with each other, helping the body be healthy in return for the food and shelter it provides. Collectively, all microorganisms inside the human body are referred to as the microbiome, most of which is located in the gastrointestinal tract.
The microbiota has coevolved over millions of years to help shape and influence human development and in particular immune defenses. Its functions are manifold, defending against harmful microorganisms, degrading toxic compounds, and teaching the immune system to tell friends from foes. It also helps with nutrition, digesting food humans aren’t able to digest by themselves, for example.
Several studies have looked at the microbiota over the years, suggesting that it plays an important role in our health. Last year, researchers from North Carolina State University found that the microbiome may have played a critical role in our ancestors’ quest to spread across the world, allowing them to survive in new geographical areas.
Now, a group of researchers at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) used a DNA-sequencing method to explore over 28,000 gut microbiome samples collected in different parts of the world. The analysis led to them identifying more than 140,000 viral species that are living in the human gut – a number much larger than what they were expecting. Perhaps most importantly, half of the viruses had never been seen before.
“Most of the viruses we found have DNA as their genetic material, which is different from the pathogens most people know, such as SARS-CoV-2 or Zika, which are RNA viruses,” Alexandre Almeida, co-author of the study, said in a statement. “These samples came mainly from healthy individuals who didn’t share any specific diseases. It’s fascinating to see how many unknown species live in our gut.”
Among a large number of viruses, the researchers identified a highly prevalent clade – a group of viruses believed to have a common ancestor and referred to in the study as Gubaphage. This was found to be the second most prevalent virus clade in the human gut, after the crAssphage, which was discovered in 2014. Both seem to infect similar types of gut bacteria, the researchers said.
Luis F. Camarillo-Guerrero, the first author of the study, highlighted the “stringent quality control” done in the study as well as the machine learning approach, which allows to mitigate contamination and obtain “highly complete” viral genomes. These, the researcher said, will help to better understand the role played by viruses in the microbiome and even lead to potential new treatments.
Using the results of the study, the researchers created the Gut Phage Database (GPD) – a highly curated database that has 142,809 non-redundant phage genomes. They believe the GPD will be a valuable resource for other researchers studying bacteriophages and the role they play in regulating the health of both our gut bacteria and ourselves.
“Having a comprehensive database of high-quality phage genomes paves the way for a multitude of analyses of the human gut virome at a greatly improved resolution, enabling the association of specific viral clades with distinct microbiome phenotypes. Importantly, GPD provides a blueprint to guide functional and phenotypic experiments of the human gut phageome,” the researchers wrote in the study.
The study was published in the journal Cell.