World-first database catalogs 1,000s of viruses in our gut microbiome
Researchers from Ohio State University have created the first catalog of viral populations known to inhabit the human gut. Called the Gut Virome Database, the study suggests each person’s gut viral population is as unique as their fingerprints.
Our gut microbiome has become a major focus of research over the past few years after the trillions of micro-organisms living in out digestive system were found to play a key role in maintaining human health. The vast majority of these organisms in our gut are bacteria, but the gut microbiome isn’t just a massive bacterial population – it also consists of parasites, fungi and viruses.
Cataloging these other microbiome inhabitants is not easy. Viruses, unlike bacteria, lack any universal genomic markers. In fact, anywhere from 40 to 90 percent of viral genomic sequences are known as “viral dark matter,” meaning they don’t align with any known reference virus sequences.
So the first step for the researchers was to compile data from dozens of prior studies looking at viruses in the human gut. The ultimate dataset compiled encompassed nearly 2,000 people spanning 16 countries.
"We used machine learning on known viruses to help us identify the unknown viruses," explains first author, Ann Gregory. "We were interested in how many types of viruses we could see in the gut, and we determined that by how many types of genomes we could see since we couldn't visually see the viruses."
The study ended up cataloging 33,242 unique viral populations, establishing a new, open-source reference resource called the Gut Virome Database.
To establish the effectiveness of the new database the researchers looked for patterns in the data. They initially discovered that the diversity of the virome (as a collection of viruses is called) within the gut increases with age but seems to decrease after the age of 65. This pattern resembles age-related diversity patterns seen in gut bacteria populations, but one notable exception was found. In the guts of infants with dysfunctional immune systems there seems to be notable viral diversity but limited bacterial diversity.
"A general rule of thumb for ecology is that higher diversity leads to a healthier ecosystem," says Gregory. "We know that more diversity of viruses and microbes is usually associated with a healthier individual. And we saw that healthier individuals tend to have a higher diversity of viruses, indicating that these viruses may be potentially doing something positive and having a beneficial role."
Another interesting finding from the novel research is the vast majority of viruses cataloged were phages. Also known as bacteriophages, these are extraordinarily common viruses that attach to bacteria and replicate within them.
Matthew Sullivan, senior author on the study, suggests there is a kind of symbiotic relationship between phages and bacteria in the gut microbiome and says the new Gut Virome Database will be an important tool for any researcher planning a therapeutic based around modulating the gut microbiome.
"Phages are part of a vast interconnected network of organisms that live with us and on us, and when broad-spectrum antibiotics are used to fight against infection, they also harm our natural microbiome," explains Sullivan. "We are building out a toolkit to scale our understanding and capabilities to use phages to tune disturbed microbiomes back toward a healthy state.”
The research adds another complex layer to the gut microbiome. It is unclear how these viruses may be influencing the general health of humans but the researchers do note this study reveals there to be no core group of viruses common to the guts of all humans.
In fact, the diversity of the gut virome is such that each person’s individual viral population may be as unique as their fingerprints. Co-author on the study Oliver Zablocki says this novel database is the first step towards working out whether gut viruses cause human disease, or whether they are merely influenced by disease.
“I see it as the chicken and the egg,” says Zablocki. “We see the disease and we see the community structure. Was it because of this community structure that the disease occurred, or is the disease causing the community structure that we see? This standardized dataset will enable us to pursue those questions.”
The new research was published in the journal Cell Host & Microbe.
Source: Ohio State University