Each human gut has a viral 'fingerprint'
New database consists of over 33,000 unique viral populations in the gut


Date:
August 24, 2020
Source:
Ohio State University
Summary:
Each person's gut virus composition is as unique as a fingerprint,
according to the first study to assemble a comprehensive database
of viral populations in the human digestive system.



FULL STORY ==========================================================================
Each person's gut virus composition is as unique as a fingerprint,
according to the first study to assemble a comprehensive database of
viral populations in the human digestive system.


==========================================================================
An analysis of viruses in the guts of healthy Westerners also showed
that dips and peaks in the diversity of virus types between childhood
and old age mirror bacterial changes over the course of the lifespan.

The Gut Virome Database developed by Ohio State University scientists identifies 33,242 unique viral populations that are present in the
human gut.

(A collection of viruses like those in the human gut is called a
virome.) This is not cause for alarm: Most viruses don't cause disease.

In fact, the more scientists learn about viruses, the more they see them
as part of the human ecosystem -- suggesting viruses have potential
to represent a new class of drugs that could fight disease-causing
bacteria, especially those resistant to antibiotics. Better knowledge of viruses in the gut environment could even improve understanding of the gastrointestinal symptoms experienced by some of the sickest COVID-19
patients.

The researchers plan to update the open-access database on a regular
basis.

"We've established a robust starting point to see what the virome looks
like in humans," said study co-author Olivier Zablocki, a postdoctoral researcher in microbiology at Ohio State. "If we can characterize
the viruses that are keeping us healthy, we might be able to harness
that information to design future therapeutics for pathogens that can't otherwise be treated with drugs." The study is published today (Aug. 24)
in the journal Cell Host & Microbe.



==========================================================================
Talk of the good and bad bacteria in the gut microbiome is commonplace
these days, but viruses in the gut -- and everywhere -- are hard to
detect because their genomes don't contain a common signature gene
sequence that bacteria genomes do. So much of the vast sequence space of viruses remains unexplored that it is often referred to as "dark matter."
For this work, the researchers started with data from 32 studies over
about a decade that had looked at gut viruses in a total of 1,986 healthy
and sick people in 16 countries. Using techniques to detect virus genomes,
the team identified more than 33,000 different viral populations.

"We used machine learning on known viruses to help us identify the unknown viruses," said first author Ann Gregory, who completed this work while
she was a graduate student at Ohio State. "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." Their analysis confirmed findings from smaller studies suggesting that though a few viral populations were shared within a subset
of people, there is no core group of gut viruses common to all humans.

A few trends were identified, however. In healthy Western individuals,
age influences the diversity of viruses in the gut, which increases significantly from childhood to adulthood, and then decreases after
age 65. The pattern matches what is known about ebbs and flows of gut
bacterial diversity with one exception: Infant guts with underdeveloped
immune systems are teeming with a range of virus types, but few bacteria varieties.



========================================================================== People living in non-Western countries had higher gut virus diversity
than Westerners. Gregory said other research has shown that non-Western individuals who move to the United States or another Western country
lose that microbiome diversity, suggesting diet and environment drive
virome differences. (For example, the scientists found some intact plant viruses in the gut -- the only way for them to get there is through the
diet.) Variations in viral diversity could also be seen in healthy versus
sick participants in the 32 studies analyzed.

"A general rule of thumb for ecology is that higher diversity leads to
a healthier ecosystem," Gregory said. "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." Almost all of
the populations -- 97.7 percent -- were phages, which are viruses that
infect bacteria. Viruses have no function without a host -- they drift
in an environment until they infect another organism, taking advantage
of its properties to make copies of themselves. The most-studied viruses
kill their host cells, but scientists in the Ohio State lab in which
Gregory and Zablocki worked have discovered more and more phage-type
viruses that coexist with their host microbes and even produce genes
that help the host cells compete and survive.

The leader of that lab, senior study author Matthew Sullivan, has his
sights set on "phage therapy" -- the 100-year-old idea of using phages
to kill antibiotic-resistant pathogens or superbugs.

"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,"
Sullivan said. "We are building out a toolkit to scale our understanding
and capabilities to use phages to tune disturbed microbiomes back toward
a healthy state.

"Importantly, such a therapeutic should impact not only our human
microbiome, but also that in other animals, plants and engineered systems
to fight pathogens and superbugs. They could also provide a foundation
for something we might have to consider in the world's oceans to combat
climate change." A professor of microbiology and civil, environmental and geodetic engineering, Sullivan has helped establish cross-disciplinary
research collaborations at Ohio State. He recently founded and directs
Ohio State's new Center of Microbiome Science and co-directs the
Infectious Diseases Institute's Microbial Communities program.

Zablocki noted that there is still a lot to learn about the functions
of viruses in the gut -- both beneficial and harmful.

"I see it as the chicken and the egg," he said. "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." This work was supported by the Ohio Supercomputer
Center and funded by the Gordon and Betty Moore Foundation, the National Institutes of Health and Ohio State's Center of Microbiome Science.


========================================================================== Story Source: Materials provided by Ohio_State_University. Original
written by Emily Caldwell. Note: Content may be edited for style and
length.


========================================================================== Journal Reference:
1. Ann C. Gregory, Olivier Zablocki, Ahmed A. Zayed, Allison Howell,
Benjamin Bolduc, Matthew B. Sullivan. The Gut Virome Database
Reveals Age-Dependent Patterns of Virome Diversity in the Human
Gut. Cell Host & Microbe, 2020; DOI: 10.1016/j.chom.2020.08.003 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200824131803.htm

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