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Just read about an international study that discussed how millions of bacteria and viruses circle the earth in the earth's atmosphere every day, and get deposited on land by rain and dust particles. Which could explain why similar viruses and bacteria are found in totally different environments in different parts of the world. The study measured what was deposited high in the mountains of the Sierra Nevada, but one would expect microbes to be deposited everywhere, not just in high mountains. We are surrounded by microbes! (Another post on this topic.) From Astrobiology:

Most Viruses And Bacteria Fall From The Sky

An international research project led by the University of Granada has revealed for the first time that almost one billion viruses and more than twenty million bacteria circulate in the Earth's atmosphere and are deposited in high-mountain places every day. The research findings, published recently in the ISME Journal: Multidisciplinary Journal of Microbial Ecology (part of the Nature group) help to explain why genetically identical viruses have been found in such distant locations and diverse environments of the planet. The University of British Columbia (Canada) and San Diego State University (United States) also participated in the project.  ...continue reading "Viruses and Bacteria Circle the Earth and Fall In Rain and Dust"

Image result for permafrost  There are many posts on this site about the microbes within us (the microbiome) or around us, but the following article may be a real eye opener. Due to the permafrost melting (as in Alaska, northern Canada, Siberia, etc) from global warming, old infectious viruses and bacteria might be released from the thawing permafrost. This is what recently happened in Siberia, where melting permafrost released anthrax spores which killed 2300 reindeer and a 12 year old boy, and sickened at least 20 other people. From Scientific American:

As Earth Warms, the Diseases That May Lie Within Permafrost Become a Bigger Worry

This past summer anthrax killed a 12-year-old boy in a remote part of Siberia. At least 20 other people, also from the Yamal Peninsula, were diagnosed with the potentially deadly disease after approximately 100 suspected cases were hospitalized. Additionally, more than 2,300 reindeer in the area died from the infection. The likely cause? Thawing permafrost. According to Russian officials, thawed permafrost—a permanently frozen layer of soil—released previously immobile spores of Bacillus anthracis into nearby water and soil and then into the food supply. The outbreak was the region's first in 75 years.

Researchers have predicted for years that one of the effects of global warming could be that whatever is frozen in permafrost—such as ancient bacteria—might be released as temperatures climb. This could include infectious agents humans might not be prepared for, or have immunity to, the scientists said. Now they are witnessing the theoretical turning into reality: infectious microorganisms emerging from a deep freeze....In a 2011 paper published in Global Health Action, co-authors Boris A. Revich and Marina A. Podolnaya wrote of their predictions: “As a consequence of permafrost melting, the vectors of deadly infections of the 18th and 19th centuries may come back, especially near the cemeteries where the victims of these infections were buried.”

And permafrost is indeed thawing—at higher latitudes and to greater depths than ever before....What thawing permafrost could unleash depends on the heartiness of the infectious agent involved. A lot of microorganisms cannot survive in extreme cold, but some can withstand it for many years. “B. anthracis are special because they are sporulating bacteria,” says Jean-Michel Claverie, head of the Mediterranean Institute of Microbiology and a professor at Aix-Marseille University in France. “Spores are extremely resistant and, like seeds, can survive for longer than a century.”

Viruses could also survive for lengthy periods. In 2014 and 2015 Claverie and his colleague Chantal Abergel published their findings on two still infectious viruses from a chunk of 30,000-year-old Siberian permafrost. Although Pithovirus sibericum and Mollivirus sibericum can infect only amoebas, the discovery is an indication that viruses that infect humans—such as smallpox and the Spanish flu—could potentially be preserved in permafrost.

Human viruses from even further back could also make a showing. For instance, the microorganisms living on and within the early humans who populated the Arctic could still be frozen in the soil. “There are hints that Neandertals and Denisovans could have settled in northern Siberia [and] were plagued by various viral diseases, some of which we know, like smallpox, and some others that might have disappeared,” Claverie says....Janet Jansson, who studies permafrost at the Pacific Northwest National Laboratory in Washington State, is not worried about ancient viruses. Several attempts to discover these infectious agents in corpses have come up empty, she notes. 

In effect, infectious agents buried in the permafrost are unknowable and unpredictable in their timing and ferocity. Thus, researchers say thawing permafrost is not our biggest worry when it comes to infectious diseases and global warming. The more immediate, and certain, threat to humans is the widening geographical ranges of modern infectious diseases (and their carriers, such as mosquitoes) as the earth warms. “We now have dengue in southern parts of Texas,” says George C. Stewart, McKee Professor of Microbial Pathogenesis and chair of the department of veterinary pathobiology at the University of Missouri. “Malaria is seen at higher elevations and latitudes as temperatures climb. And the cholera agent, Vibrio cholerae, replicates better at higher temperatures.”

 Bacillus anthracis - Anthrax bacteria  Credit:Wikipedia

Image result for anthrax disease, wiki Skin anthrax lesion on the neck  Credit:Wikipedia

 Image result for toddlers 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.

"We were surprised that right from the beginning quite a diversity of viruses was found in the gut," said Holtz, also a pediatric gastroenterologist who treats patients at St. Louis Children's Hospital. "It prompts the question—where do these viruses come from? We don't know yet whether diet, method of the baby's delivery or other environmental influences play a role."

Analyzing genomic material in the stool samples, the researchers noted that some of the viruses they identified are known to infect cells of the human host, but others actually infect the bacteria. In fact, the researchers found that the kinds of viruses that infect bacteria, not human cells, were the most rich and diverse earliest in an infant's life and then their numbers declined. They also showed that strains of bacteria did the opposite, starting out with low numbers early and becoming more diverse as the babies grew into their toddler years.

The investigators suspect that the changes in population dynamics they observed in these viruses and bacteria are caused by a predator-prey relationship. The viruses that exclusively kill bacteria are called bacteriophage, literally "bacteria eater." The early diversity of bacteriophage means lots of predators with no prey. Since bacteriophage can't survive without their bacterial prey, the high bacteriophage numbers quickly go down. Faced with few predators, bacteria are then free to flourish and colonize the gut. "The predator-prey dynamic is still a hypothesis at this point," Holtz said. 

The researchers also observed a relatively large diversity of a type of virus that infects human cells called anellovirus. Anelloviruses are of interest to researchers because they appear to reflect a person's immune status, with more viruses present when the immune system is weaker"One child had at least 47 anellovirus strains at the 12-month sampling," Holtz said. "It's important to remember that these are healthy children living in the community. 

The researchers also noted that almost all of the anelloviruses identified in this study were previously unknown. Such data, originating from only eight babies in St. Louis, hints at the size and difficulty of the task of even determining a healthy baseline for the virome. Such a baseline is required before scientists can understand what roles gut viromes may play in conditions like obesity, diabetes, colitis and Crohn's disease."At this point, we're just trying to establish what is normal," Holtz said. 

 Various viruses.Credit:National Geographic

This nice general summary of what scientists know about the microbial community within us was just published by a division of the NIH (National Institutes of Health). Very simple and basic. From the National Institute of General Medical Sciences (NIGMS):

Facts about our microbial menagerie

Trillions of microorganisms inhabit us -- inside and out. Scientists are surveying these microbial metropolises to learn more about their role in health. Microbiologists Darren Sledjeski of the National Institutes of Health (NIH) and Andrew Goodman of Yale University share a few details of what researchers have learned so far.

1. The majority of the microbes that inhabit us are bacteria. The rest of the microbial menagerie is fungi and viruses, including ones that infect the bacteria! Collectively, our resident microorganisms are referred to as the human microbiota, and their genomes are called the human microbiome.

2. Our bodies harbor more bacterial cells than human ones. Even so, the microbiota accounts for less than 3 percent of a person's body mass. That's because our cells are up to 10,000 times bigger in volume than bacterial cells.

3. Your collection of bacteria has more genes than you do. Scientists estimate that the genomes of gut bacteria contain 100-fold or more genes than our own genomes. For this reason, the human microbiome is sometimes called our second genome.

4. Most of our microbes are harmless, and some are helpful. For example, harmless microbes on the skin keep infectious microbes from occupying that space. Microbes in the colon break down lactose and other complex carbohydrates that our bodies can't naturally digest.

5. Different microbes occupy different parts of the body. Some skin bacteria prefer the oily nooks near the nose, while others like the dry terrain of the forearm. Bacteria don't all fare well in the same environment and have adapted to live in certain niches.

6. Each person's microbiota is unique. The demographics of microbiota differ among individuals. Diet is one reason. Also, while a type of microbe might be part of one person's normal microbial flora, it might not be part of another's, and could potentially make that person sick.

7. Host-microbial interactions are universal. Microbial communities may vary from person to person, but everyone's got them, including other creatures. For this reason, researchers can use model organisms to tease apart the complexities of host-microbial interactions and develop broad principles for understanding them. The mouse is the most widely used animal model for microbiome studies.

8. The role of microbiota in our health isn't entirely clear. While it's now well accepted that the microbial communities that inhabit us are actively involved in a range of conditions -- from asthma to obesity -- research studies have not yet pinpointed why or how. In other words, the results may suggest that the presence of a bacterial community is associated with a disease, but they don't show cause and effect.

9. Most of our microbes have not been grown in the lab. Microbes require a certain mix of nutrients and other microbes to survive, making it challenging to replicate their natural environments in a petri dish. New culturing techniques are enabling scientists to study previously uncultivated microbes.

10. The impact of probiotic and prebiotic products isn't clear. Fundamental knowledge gaps remain regarding how these products may work and what effects they might have on host-microbial interactions. A new NIH effort to stimulate research in this area is under way.

11. There's even more we don't know! Additional areas of research include studying the functions of microbial genes and the effects of gut microbes on medicines. The more we learn from these and other studies, the more we'll understand how our normal microbiota interacts with us and how to apply that knowledge to promote our health.

Lactobacillus sp 01.pngLactobacillus (the rods) near a squamous epithelial cell      Photo from CDC 

Amazing persistence of the restroom microbial community.From NPR news:

What Microbes Lurked In The Last Public Restroom You Used?

The invisible world of the bathroom isn't pretty — unless you're a microbe. After scanning the microbial zoo of four public restrooms recently, a team of researchers found a diverse swarm of characters that persisted for months despite regular cleaning of the facilities. The goal of the study, published in the December issue of Applied and Environmental Microbiology, was to better understand how communities of bacteria and viruses can shift in these very public places across a couple of months.

To get their down-and-dirty readings, the researchers selected four bathrooms at San Diego State University... They checked two women's restrooms and two men's restrooms (a high-traffic and a low-traffic bathroom for each gender). The bathrooms were thoroughly cleaned at the study's start with bleach solution, which killed any existing germ communities.Then, during the following hours, days, weeks and months of human use, the researchers periodically swabbed soap dispensers, floors and toilet seats in all four restrooms for microbe samples. 

Within one hour of sterilization, the bathrooms were completely recolonized with microbes — just as plants rapidly arrive and populate a newly emerged island. Fecal bacteria dominated, including on toilet seats and on soap dispensers — about 45 percent of the bacteria there were of fecal origin.

In all, the scientists found genetic traces of more than 77,000 distinct types of bacteria and viruses. (At least some of those species were likely dead or dormant, the scientists add; genetic testing detects them all, whatever their status.)

Patterns of regrowth and succession, as some species waned and others replaced them, were surprisingly similar from bathroom to bathroom; within just five hours the population mix in each room stabilized.

When the team tried growing cultures from different surfaces in each room, they found one set of live bacteria in overwhelming abundance: Staphylococcus. Staph's persistence in these studies points to its power as a potential pathogen, Gilbert says. Various versions are common on human skin and inside the nose and other orifices; they generally cause no problems, or trigger only minor skin infections. But staph infections can be serious, or even kill, if the bacteria get into bloodstream, joints, bones, lungs or heart

Gilbert notes that none of the live Staph strains detected in the San Diego bathrooms showed signs of being antibiotic resistant. They were instead relatively harmless "skin bugs that happened to have lost their skin," he says. The team did find genes from MRSA hiding on the floor, as well as traces of some troublemaker viruses, including HPV and herpes virus.

Interestingly, although restrooms that were left open for use for up to two months were cleaned regularly with soap and water, the communities of microbes found there remained relatively unchanged for the full eight weeks of the study.

No need to be scared or grossed out by that finding, Gilbert says..."All human environments contain pathogens — your bedroom, the phone you're talking on, even the bugs inside of you could turn pathogenic at any time," Gilbert tells Shots. "But we desperately need them in our lives." Having a healthy community of good — or even just neutral — microbes can crowd out the bad ones. As we've learned from using broad-spectrum antibiotics in the human body, "sterilization is not necessarily good," he says. "Bacteria come back right away, and they might come back perturbed."

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.

Reading this is almost guaranteed to make you want to wash your hands. From Science Daily:

How quickly viruses can contaminate buildings -- from just a single doorknob

Using tracer viruses, researchers found that contamination of just a single doorknob or table top results in the spread of viruses throughout office buildings, hotels, and health care facilities. Within 2 to 4 hours, the virus could be detected on 40 to 60 percent of workers and visitors in the facilities and commonly touched objects.

There is a simple solution, though, says Charles Gerba of the University of Arizona, Tucson, who presented the study. "Using disinfecting wipes containing quaternary ammonium compounds (QUATS) registered by EPA as effective against viruses like norovirus and flu, along with hand hygiene, reduced virus spread by 80 to 99 percent," he says.

Norovirus is the most common cause of acute gastroenteritis in the United States, according to the Centers for Disease Control and Prevention (CDC). Each year, it causes an estimated 19-21 million illnesses and contributes to 56,000-71,000 hospitalizations and 570-800 deaths. Touching surfaces or objects contaminated with norovirus then putting your fingers in your mouth is a common source of infection.

In the study, Gerba and his colleagues used bacteriophage MS-2 as a surrogate for the human norovirus, as it is similar in shape, size and resistance to disinfectants. The phage was placed on 1 to 2 commonly touched surfaces (door knob or table top) at the beginning of the day in office buildings, conference room and a health care facility. After various periods of time (2 to 8 hours) they sampled 60 to 100 fomites, surfaces capable of carrying infectious organisms (light switches, bed rails, table tops, countertops, push buttons, coffee pots handles, sink tap handles, door knobs, phones and computer equipment), for the phages.

"Within 2 to 4 hours between 40 to 60% of the fomites sampled were contaminated with virus," says Gerba.

In the intervention phase cleaning personal and employees were provided with QUATS disinfectant containing wipes and instructed on proper use (use of at least once daily). The number of fomites on which virus was detected was reduced by 80% or greater and the concentration of virus reduced by 99% or more.

We know so little about the viruses in the human microbiome that a study just reported a newly discovered gut virus found in most of the world's population. From Medical Xpress:

Newly discovered gut virus lives in half the world's population

Odds are, there's a virus living inside your gut that has gone undetected by scientists for decades. A new study led by researchers at San Diego State University has found that more than half the world's population is host to a newly described virus, named crAssphage, which infects one of the most common types of gut bacteria, Bacteroidetes. This phylum of bacteria is thought to be connected with obesity, diabetes and other gut-related diseases.

The fact that it's so widespread indicates that it probably isn't a particularly young virus, either. "We've basically found it in every population we've looked at," Edwards said. "As far as we can tell, it's as old as humans are." He and his team named the virus crAssphage, after the cross-assembly software program used to discover it.

Some of the proteins in crAssphage's DNA are similar to those found in other well-described viruses. That allowed Edwards' team to determine that their novel virus is one known as a bacteriophage, which infects and replicates inside bacteria—and using innovative bioinformatic techniques, they predicted that this particular bacteriophage proliferates by infecting a common phylum of gut bacteria known as Bacteriodetes.

 Further details about crAssphage have been difficult to come by. It's unknown how the virus is transmitted, but the fact that it was not found in very young infants' fecal samples suggests that it is not passed along maternally, but acquired during childhood.

A topic that is rarely mentioned is the human virome (the collection of resident viruses in the human body). We all have many viruses, but almost nothing is known about them.This is an introductory article about the human virome. From the January 11, 2014 Science News:

The vast virome

 The microbiome — what scientists refer to as the collection of bacteria, fungi and other single-celled organisms that live in and on the body — has been a hot research topic for more than a decade. But bacteria aren’t the only microbes with which we humans share space.

The most abundant inhabitants of what many researchers are calling “the human ecosystem” are the virusesViruses are deceptively simple organisms consisting of genetic material packed in a protein shell. They are tiny and can’t replicate on their own, relying on human or other cells to reproduce.

And yet, scientists estimate that 10 quintillion virus particles populate the planet. That’s a one followed by 31 zeros. They outnumber bacteria 10-to-1 in most ecosystems. And they’re ubiquitous in and on humans.

Pérez-Brocal and others are learning that viruses, once seen only as foreign invaders that make people sick, are an integral part of human biology. Some cause major diseases, including influenza, AIDS and some cancers. Others, conversely, may promote health. Some may even help us gauge how well the human immune system works.

The study of people’s resident viruses, known collectively as the human virome, is “a whole new frontier in the understanding of humans,” and could become important for the future of medicine, says Forest Rohwer, an environmental microbiologist at San Diego State University.

Rohwer’s research indicates that viruses are part of the human defense system. Mucus studded with bacteria-infecting viruses called bacteriophage, or phage, may help protect host cells from invasive microbes, he and his colleagues reported June 25 in the Proceedings of the National Academy of Sciences. 

“We know a lot about the bacteria that inhabit humans,” says David Pride, an infectious disease doctor at the University of California, San Diego. In comparison, “we know absolutely nothing about the viruses.” Not that scientists haven’t been interested in viruses. Until recently there was just no good way to identify them, an important first step toward understanding the biology of health and disease. As a consequence, virome research is in its infancy.

Researchers have gotten a head start on cataloging bacterial denizens of the body because all bacterial cells contain a version of the 16S ribosomal RNA gene. Virus hunters aren’t so lucky. There is no analogous virus-identification tag. Instead, to look for viruses, researchers must sequence hundreds of thousands of bits of DNA from a sample — skin swabs, saliva, feces or mucus, for example. Scientists have gotten really good at generating these DNA sequences; the trick is figuring out what they are.

Every time Frederic Bushman samples a new person’s virome, he says, he finds new viruses. A microbiologist at the University of Pennsylvania Perelman School of Medicine in Philadelphia, Bushman has shown that no two people’s gut viruses are exactly alike. But once a person has picked up a community of bacteria-infecting phage, it tends to stick around. Fully 80 percent of the viruses present when the researchers first started tracking one man’s virome were still there more than two years later.

Maybe researchers can use bacteriophage to shape the human microbiome in healthier ways. Using phage to control bacteria is a resurgence of an old idea. In the 1920s, doctors in the former Soviet Union and other Eastern European countries began using phage to treat specific bacterial infections. Unlike antibiotics, which kill bacteria indiscriminately, phage target only certain microbes for destruction.

“Healthy subjects are just loaded with viruses,” Wylie says. Even viruses known to cause diseases such as the common cold were found in healthy kids. That makes it difficult to determine whether a particular virus is really making someone sick.

Some viruses previously thought innocent may cause harmTo figure out which viruses are friends, foes or neutral passengers on the human body, scientists first need to identify them. Researchers still aren’t very good at recognizing new viruses, says Brian Jones, a molecular biologist at the University of Brighton in England. 

Based on what researchers have learned so far about the virome, Jones is convinced that viruses and other microbes “should be viewed as a part of us rather than something that lives in or on us.” They are part of the puzzle, the intricate ecosystem composed of human and microbial cells, all pushing and pulling at one another and subject to local conditions, such as diet and environment.