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Yes, even healthy newborns have a diversity of viruses in the gut - this is their virome (community of viruses), and it undergoes changes over time. In fact, the entire infant microbiome (community of microbes) is highly dynamic and the composition of bacteria, viruses and bacteriophages changes with age. One interesting finding is that initially newborn babies have a lot of bacteriophages (viruses that infect bacteria), but that these decline over the first two years of age. From Medical Xpress:

Viruses flourish in guts of healthy babies

Bacteria aren't the only nonhuman invaders to colonize the gut shortly after a baby's birth. Viruses also set up house there, according to new research at Washington University School of Medicine in St. Louis. All together, these invisible residents are thought to play important roles in human health.The study, published online Sept. 14 in Nature Medicine, reports data from eight healthy infants and is one of the first surveys of viruses that reside in the intestine. The investigators analyzed stool samples to track how the babies' bacterial gut microbiomes and viromes changed over the first two years of life.

"We are just beginning to understand the interplay between all the different types of life within our gut," said senior author Lori R. Holtz, MD, assistant professor of pediatrics. "They are not stand-alone communities. We also are seeing that the environment of the infant gut is extremely dynamic, which differs from the relative stability that has been shown in adults."The earliest stool samples were taken at 1-4 days of life, and even at this early time point, Holtz noted, viruses were present ...continue reading "Viruses Live in The Guts of Healthy Babies"

Exciting research in a new area - our trillions of viruses or virome. From the new research it looks like some of the viruses are beneficial to us and help keep us healthy. It's time to stop thinking of all viruses (and bacteria) as bad, but instead that some viruses are necessary for good health. From Science Daily:

Natural Gut Viruses Join Bacterial Cousins in Maintaining Health and Fighting Infections

Microbiologists at NYU Langone Medical Center say they have what may be the first strong evidence that the natural presence of viruses in the gut -- or what they call the 'virome' -- plays a health-maintenance and infection-fighting role similar to that of the intestinal bacteria that dwell there and make up the "microbiome."

In a series of experiments in mice that took two years to complete, the NYU Langone team found that infection with the common murine norovirus, or MNV, helped mice repair intestinal tissue damaged by inflammation and helped restore the gut's immune defenses after its microbiome had been wiped out by antibiotic therapy. In a report on their work to be published in the journal Nature online Nov. 19, researchers say they also found that MNV bolstered the immune system in fighting off tissue damage.

"Our research offers compelling data about the mutually supportive relationship between viruses and bacteria in the mouse gut and lays the groundwork for further research on precisely how the virome supports the immune system, which likely applies to humans, as well," says senior study investigator Ken Cadwell, PhD, an assistant professor at NYU Langone.

"We have known for a long time that people get infected all the time with viruses and bacteria, and they don't get sick," says Cadwell. "Now we have scientific evidence that not every viral infection is bad, but may actually be beneficial to health, just as we know that many bacterial infections are good for maintaining health."

According to Cadwell, until now, scientists have had mostly trace genetic evidence of a virome's existence, but none to confirm its normal presence in the gut or to clarify whether it plays a harmful, neutral, or helpful role.

What the NY Times had to say about this new area of research:

Viruses as a Cure

When we talk about viruses, usually we focus on the suffering caused by Ebola, influenza, and the like. But our bodies are home to trillions of viruses, and new research hints that some of them may actually be keeping us healthy.

“Viruses have gotten a bad rap,” said Ken Cadwell, an immunologist at New York University School of Medicine. “They don’t always cause disease.” Dr. Cadwell stumbled by accident onto the first clues about the healing power of viruses. At the time, he was studying the microbiome, the community of 100 trillion microbes living in our bodies. Scientists have long known that the microbiome is important to our health.

Kristine Wylie, a research instructor of pediatrics at Washington University School of Medicine who was not involved in the research, speculated that in real life, certain viruses might be important partners with the microbiome. “It isn’t hard to imagine that the viral exposures we get as children are important to our development,” she said.

This exciting new research is just the beginning knowledge about our virome (the virus community within us). Note that they only looked at viruses in a few areas of our bodies - the rest is still a mystery. But note that it is normal for healthy individuals to carry viruses, and that we have "distinct viral fingerprints". We don't know if the viruses are beneficial or not to us at this time. From Science Daily:

Healthy humans make nice homes for viruses

The same viruses that make us sick can take up residence in and on the human body without provoking a sneeze, cough or other troublesome symptom, according to new research. On average, healthy individuals carry about five types of viruses on their bodies, the researchers report. The study is the first comprehensive analysis to describe the diversity of viruses in healthy people.

The research was conducted as part of the Human Microbiome Project, a major initiative funded by the National Institutes of Health (NIH) that largely has focused on cataloging the body's bacterial ecosystems. ..."Lots of people have asked whether there is a viral counterpart, and we haven't had a clear answer. But now we know there is a normal viral flora, and it's rich and complex."

In 102 healthy young adults ages 18 to 40, the researchers sampled up to five body habitats: nose, skin, mouth, stool and vagina. The study's subjects were nearly evenly split by gender.

At least one virus was detected in 92 percent of the people sampled, and some individuals harbored 10 to 15 viruses...."We only sampled up to five body sites in each person and would expect to see many more viruses if we had sampled the entire body."

Scientists led by George Weinstock, PhD, at Washington University's Genome Institute, sequenced the DNA of the viruses recovered from the body, finding that each individual had a distinct viral fingerprint. (Weinstock is now at The Jackson Laboratory in Connecticut.) About half of people were sampled at two or three points in time, and the researchers noted that some of the viruses established stable, low-level infections.

The researchers don't know yet whether the viruses have a positive or negative effect on overall health but speculate that in some cases, they may keep the immune system primed to respond to dangerous pathogens while in others, lingering viruses increase the risk of disease.

Study volunteers were screened carefully to confirm they were healthy and did not have symptoms of acute infection. They also could not have been diagnosed in the past two years with human papillomavirus infection (HPV), which can cause cervical and throat cancer, or have an active genital herpes infection.

Analyzing the samples, the scientists found seven families of viruses, including strains of herpes viruses that are not sexually transmitted. For example, herpesvirus 6 or herpesvirus 7 was found in 98 percent of individuals sampled from the mouth. Certain strains of papillomaviruses were found in about 75 percent of skin samples and 50 percent of samples from the nose. Novel strains of the virus were found in both sites.

Not surprisingly, the vagina was dominated by papillomaviruses, with 38 percent of female subjects carrying such strains. Some of the women harbored certain high-risk strains that increase the risk of cervical cancer. These strains were more common in women with communities of vaginal bacteria that had lower levels of Lactobacillus and an increase in bacteria such as Gardnerella, which is associated with bacterial vaginosis.

Adenoviruses, the viruses that cause the common cold and pneumonia, also were common at many sites in the body.