Everyone poops his or her own viruses

Scientists have conducted a new kind of gut check — one that catalogs viruses found in the intestines of identical twins and their mothers.

The work suggests that each person has a distinctive mix of viruses in their feces, and that mix doesn’t change much over time, say researchers led by Jeffrey Gordon of Washington University School of Medicine in St. Louis. The new study, which appears in the July 15 Nature, also suggests that viruses and bacteria in the gut aren’t engaging in the molecular arms races that usually characterize how microbes and their viral predators relate to each other.

The new work grew out of the Human Microbiome Project, which seeks to catalog the genetic diversity of bacteria, archaea, and other microbes living in and on the human body.  Gordon’s virome project (for viral genome) identified hundreds of types of viruses, about 80 percent of which were not previously known.  Most of them are bacteriophages — viruses that attack bacteria.

Gordon and his colleagues have previously characterized the bacteria and other microbes living in the gut. That work revealed that although each person’s intestines contain about 800 different bacterial species, family members tend to have more similar bacterial mixes than unrelated people do. But the new study could not find such a family resemblance in the viruses isolated from frozen fecal samples of four sets of identical twins and their mothers.

Each person’s viral mix stayed relatively stable over the course of a year. “Ultimately, this kind of stability indicates it’s part of our biology,” says Martin Blaser, a microbiologist and physician at New York University’s Langone Medical Center. “Now we have to figure out what it means.”

Relationships between viruses and bacteria in human intestines may be friendlier than in other environments such as sewage sludge, the study suggests. Bacteriophages generally change their genetic repertoire rapidly to keep up with their bacterial prey’s ever-morphing defenses. But Gordon’s team found that bacteriophages in the intestines change their genetic makeup very little.

When the researchers probed deeper, they found that many of the bacteriophages carried bacterial genes that help microbes survive the anaerobic conditions in the colon.

“You could see that these viruses were porting around genes that could benefit their host bacteria,” Gordon says. If the viruses transfer those genes to other bacteria that don’t normally carry them, that could help genetically disadvantaged bacteria evolve to live better in the colon.

More research could reveal whether people do actually bear some family resemblance in their fecal viruses, Blaser says. “It’s a beginning,” he says of the virus catalog. 

Gordon’s team now plans to explore more people’s viromes. Experiments in mice may also help the researchers learn how viruses influence the composition of intestinal bacteria.