Using metagenomics tools, which sequence all of the viral material in a sample, researchers have investigated the viruses that call the human gut home. Viruses are everywhere in the environment, and an astonishing 140,000 species of viruses have been found in samples from the human gastrointestinal tract. Many of these viruses are bacteriophages, which infect bacterial cells. Over half of these viruses have never been characterized before, and the vast majority are not harmful, and probably serve important functions. The findings have been reported in Cell.
In this work, the researchers assessed more than 28,000 microbiome samples that were gathered from individuals living in different parts of the world, and the genomic sequences of 2,898 species of bacteria isolated from the human gut. This effort shows that the human gut is an environment that is incredibly diverse, and we still have a lot to learn about it and how the gut microbiome affects our health. For example, these many viruses could be playing a crucial role in our health.
"It's important to remember that not all viruses are harmful, but represent an integral component of the gut ecosystem. For one thing, 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. Secondly, 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, and to try and unravel the link between them and human health," explained Dr. Alexandre Almeida, Postdoctoral Fellow at the European Bioinformatics Institute (EMBL-EBI) and the Wellcome Sanger Institute.
The gut microbiome is well known as a crucial player in our health and well-being, and imbalances in the gut microbiome have been associated with disease. The many species of microorganisms in the gut means that we have a lot of research ahead of us if we're going to understand exactly how it all works.
One group of viruses among the many that were discovered in this study is a highly prevalent clade (a group of organisms that's thought to have a common ancestor). The authors have termed this clade Gubaphage; it's thought to be the second most common clade of viruses in the human gut. The most prevalent is crAssphage, which was identified in 2014.
Both of these viruses seem to infect similar types of human gut bacteria, but without further research, it is difficult to know the exact functions of the newly discovered Gubaphage.
"An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality," noted first study author Dr. Luis F. Camarillo-Guerrero of the Wellcome Sanger Institute. "A stringent quality control pipeline coupled with a machine learning approach enabled us to mitigate contamination and obtain highly complete viral genomes. High-quality viral genomes pave the way to better understand what role viruses play in our gut microbiome, including the discovery of new treatments such as antimicrobials from bacteriophage origin."
The data from this work was used to create the Gut Phage Database (GPD), a database containing about 142,000 different phage genomes.
"Bacteriophage research is currently experiencing a renaissance. This high-quality, large-scale catalog of human gut viruses comes at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies," said senior study author Dr. Trevor Lawley of the Wellcome Sanger Institute.