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Author: Sima

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The study was needed, but my first thought was "Duh! Of course." From Science Daily:

Fist bumping beats germ-spreading handshake

“Fist bumping” transmits significantly fewer bacteria than either handshaking or high-fiving, while still addressing the cultural expectation of hand-to-hand contact between patients and clinicians, according to a study published in the August issue of the American Journal of Infection Control...

In this study from the Institute of Biological, Environmental, and Rural Sciences at Aberystwyth University in the United Kingdom, researchers performed trials to determine if alternative greetings would transmit fewer germs than the traditional handshake. In this experiment, a greeter immersed a sterile-gloved hand into a container of germs. Once the glove was dry, the greeter exchanged a handshake, fist bump, or high-five with a sterile-gloved recipient. Exchanges randomly varied in duration and intensity of contact.

After the exchange, the receiving gloves were immersed in a solution to count the number of bacteria transferred during contact. Nearly twice as many bacteria were transferred during a handshake compared to the high-five, and significantly fewer bacteria were transferred during a fist bump than a high-five. In all three forms of greeting, a longer duration of contact and stronger grips were further associated with increased bacterial transmission.

“Adoption of the fist bump as a greeting could substantially reduce the transmission of infectious diseases between individuals,” said corresponding author, David Whitworth, PhD. This study expands on the recent call from the Journal of the American Medical Association (JAMA) to ban handshakes from the hospital environment. Healthcare providers’ hands can spread potentially harmful germs to patients, leading to healthcare-associated infections (HAIs). 

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This research illustrates how little we currently know about gut bacteria.But it did show the importance of diet. From Science Daily:

Monitoring rise and fall of the microbiome

Trillions of bacteria live in each person's digestive tract. Scientists believe that some of these bacteria help digest food and stave off harmful infections, but their role in human health is not well understood.

To help shed light on the role of these bacteria, a team of researchers led by MIT associate professor Eric Alm recently tracked fluctuations in the bacterial populations of two research subjects over a full year. The findings, described in the July 25 issue of the journal Genome Biology, suggest that while these populations are fairly stable, they undergo daily fluctuations in response to changes in diet and other factors...."To a large extent, the main factor we found that explained a lot of that variance was the diet."

There are a few thousand strains of bacteria that can inhabit the human gut, but only a few hundred of those are found in any given individual, Alm says. For one year, the two subjects in the study collected daily stool samples so bacterial populations could be measured. They also used an iPhone app to track lifestyle factors such as diet, sleep, mood, and exercise, generating a huge amount of data.

Analysis of this data revealed that dietary changes could produce daily variations in the populations of different strains of bacteria. For example, an increase in fiber correlated with a boost in the populations of Bifidobacteria, Roseburia, and Eubacterium rectale. Four strains -- including Faecalibacterium prausnitzii, which has been implicated in protecting against inflammatory bowel disease -- were correlated with eating citrus.

During the study, each of the two subjects experienced an event that dramatically altered the gut microbiome. Subject B experienced food poisoning caused by Salmonella, and Subject A traveled to a developing nation, where he experienced diarrheal illness for two weeks.

During Subject B's infection, Salmonella leapt from 10 percent of the gut microbiome to nearly 30 percent. At the same time, populations of bacteria from the phylum Firmicutes, believed to be beneficial to human health, nearly disappeared. After the subject recovered, Firmicutes rebounded to about 40 percent of the total microbiome, but most of the strains were different from those originally present.

Subject A also exhibited severe disruptions to his microbiome during his trip, but once he returned to the United States, it returned to normal. Unlike Subject B's recovery from food poisoning, Subject A's populations returned to their original composition.

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Great reason to add more rosemary and oregano to your diet. From Science Daily:

Rosemary, oregano contain diabetes-fighting compounds

The popular culinary herbs oregano and rosemary are packed with healthful compounds, and now lab tests show they could work in much the same way as prescription anti-diabetic medication, scientists report. In their new study, researchers found that how the herbs are grown makes a difference, and they also identified which compounds contribute the most to this promising trait.

Elvira Gonzalez de Mejia and colleagues point out that in 2012, type-2 diabetes affected more than 8 percent of Americans and cost the country $175 billion. ... Recent research has shown that herbs could provide a natural way to help lower glucose in blood. So Gonzalez de Mejia's team decided to take a closer look.They tested four different herbs, either greenhouse-grown or dried commercial versions, for their ability to interfere with a diabetes-related enzyme, which is also a target of a prescription drug for the disease.

They found that greenhouse herbs contained more polyphenols and flavonoids compared to the equivalent commercial herbs. But this didn't affect the concentration required to inhibit the enzyme. Commercial extracts of Greek oregano, Mexican oregano and rosemary were better inhibitors of the enzyme, required to reduce risk of type-2 diabetes, than greenhouse-grown herbs.

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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.

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I've recently posted (July 10 and 11) on how our biome (the microbial community within us) may affect our moods and brain functioning. However, the following excerpts from the article on creativity reminds us that we cannot neglect looking at our genetic history and genes. I highlighted in bold-type some of the research results. This author is the neuroscientist Nancy Andreason, who has spent decades studying creativity and where creative genius comes from, whether it is dependent on high IQ, and why it is so often accompanied by mental illness. Do go and read the whole article. From The Atlantic:

Secrets of the Creative Brain

I have spent much of my career focusing on the neuroscience of mental illness, but in recent decades I’ve also focused on what we might call the science of genius, trying to discern what combination of elements tends to produce particularly creative brains. What, in short, is the essence of creativity? Over the course of my life, I’ve kept coming back to two more-specific questions: What differences in nature and nurture can explain why some people suffer from mental illness and some do not? And why are so many of the world’s most creative minds among the most afflicted? My latest study, for which I’ve been scanning the brains of some of today’s most illustrious scientists, mathematicians, artists, and writers, has come closer to answering this second question than any other research to date.

Although many people continue to equate intelligence with genius, a crucial conclusion from Terman’s study is that having a high IQ is not equivalent to being highly creative...Subsequent studies by other researchers have reinforced Terman’s conclusions, leading to what’s known as the threshold theory, which holds that above a certain level, intelligence doesn’t have much effect on creativity: most creative people are pretty smart, but they don’t have to be that smart, at least as measured by conventional intelligence tests. An IQ of 120, indicating that someone is very smart but not exceptionally so, is generally considered sufficient for creative genius.

But if high IQ does not indicate creative genius, then what does? And how can one identify creative people for a study?...In my own version of a eureka moment, the answer finally came to me: creative people are better at recognizing relationships, making associations and connections, and seeing things in an original way—seeing things that others cannot see. 

This time around, I wanted to examine a more diverse sample of creativity, from the sciences as well as the arts...My individual jewels so far include, among others, the filmmaker George Lucas, the mathematician and Fields Medalist William Thurston, the Pulitzer Prize–winning novelist Jane Smiley, and six Nobel laureates from the fields of chemistry, physics, and physiology or medicine. 

You cannot force creativity to happen—every creative person can attest to that. But the essence of creativity is making connections and solving puzzles. 

As I hypothesized, the creative people have shown stronger activations in their association cortices during all four tasks than the controls have. This pattern has held true for both the artists and the scientists, suggesting that similar brain processes may underlie a broad spectrum of creative expression....Many creative people are polymaths, people with broad interests in many fields—a common trait among my study subjects.

So far, this study—which has examined 13 creative geniuses and 13 controls—has borne out a link between mental illness and creativity similar to the one I found in my Writers’ Workshop study. The creative subjects and their relatives have a higher rate of mental illness than the controls and their relatives do (though not as high a rate as I found in the first study), with the frequency being fairly even across the artists and the scientists. The most-common diagnoses include bipolar disorder, depression, anxiety or panic disorder, and alcoholism.

As in the first study, I’ve also found that creativity tends to run in families, and to take diverse forms. In this arena, nurture clearly plays a strong role. Half the subjects come from very high-achieving backgrounds, with at least one parent who has a doctoral degree. The majority grew up in an environment where learning and education were highly valued.

So why do these highly gifted people experience mental illness at a higher-than-average rate? Given that (as a group) their family members have higher rates than those that occur in the general population or in the matched comparison group, we must suspect that nature plays a role—that Francis Galton and others were right about the role of hereditary factors in people’s predisposition to both creativity and mental illness. We can only speculate about what those factors might be, but there are some clues in how these people describe themselves and their lifestyles.

One possible contributory factor is a personality style shared by many of my creative subjects. These subjects are adventuresome and exploratory. They take risks. Particularly in science, the best work tends to occur in new frontiers. (As a popular saying among scientists goes: “When you work at the cutting edge, you are likely to bleed.”) They have to confront doubt and rejection. And yet they have to persist in spite of that, because they believe strongly in the value of what they do. This can lead to psychic pain, which may manifest itself as depression or anxiety, or lead people to attempt to reduce their discomfort by turning to pain relievers such as alcohol.

I’ve been struck by how many of these people refer to their most creative ideas as “obvious.” Since these ideas are almost always the opposite of obvious to other people, creative luminaries can face doubt and resistance when advocating for them. ... When you have talent and see things in a particular way, you are amazed that other people can’t see it.” Persisting in the face of doubt or rejection, for artists or for scientists, can be a lonely path—one that may also partially explain why some of these people experience mental illness.

One interesting paradox that has emerged during conversations with subjects about their creative processes is that, though many of them suffer from mood and anxiety disorders, they associate their gifts with strong feelings of joy and excitement. “Doing good science is simply the most pleasurable thing anyone can do,” one scientist told me. 

As for how these ideas emerge, almost all of my subjects confirmed that when eureka moments occur, they tend to be precipitated by long periods of preparation and incubation, and to strike when the mind is relaxed—during that state we called REST. “A lot of it happens when you are doing one thing and you’re not thinking about what your mind is doing,” one of the artists in my study told me. “I’m either watching television, I’m reading a book, and I make a connection … 

Many creative people are autodidacts. They like to teach themselves, rather than be spoon-fed information or knowledge in standard educational settings. 

Creative people tend to be very persistent, even when confronted with skepticism or rejection....Of course, having too many ideas can be dangerous. One subject, a scientist who happens to be both a kite and a string, described to me “a willingness to take an enormous risk with your whole heart and soul and mind on something where you know the impact—if it worked—would be utterly transformative.” The if here is significant. Part of what comes with seeing connections no one else sees is that not all of these connections actually exist. 

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Even though it looks to be a modest effect, it is still good news. But they should have added kefir to the list of probiotic containing foods. From Science Daily:

Eating probiotics regularly may improve your blood pressure

Eating probiotics regularly may modestly improve your blood pressure, according to new research in the American Heart Association journal  Hypertension. Probiotics are live microorganisms (naturally occurring bacteria in the gut) thought to have beneficial effects; common sources are yogurt or dietary supplements.

"The small collection of studies we looked at suggest regular consumption of probiotics can be part of a healthy lifestyle to help reduce high blood pressure, as well as maintain healthy blood pressure levels," said Jing Sun, Ph.D., lead author and senior lecturer at the Griffith Health Institute and School of Medicine, Griffith University, Gold Coast, Queensland, Australia. "This includes probiotics in yogurt, fermented and sour milk and cheese, and probiotic supplements."

Analyzing results of nine high-quality studies examining blood pressure and probiotic consumption in 543 adults with normal and elevated blood pressure, researchers found:

  • Probiotic consumption lowered systolic blood pressure (the top number) by an average 3.56 millimeters of mercury (mm Hg) and diastolic blood pressure (the lower number) by an average 2.38 mm Hg, compared to adults who didn't consume probiotics.
  • The positive effects from probiotics on diastolic blood pressure were greatest in people whose blood pressure was equal to or greater than 130/85, which is considered elevated.
  • Probiotics with multiple bacteria lowered blood pressure more than those with a single bacteria.

We believe probiotics might help lower blood pressure by having other positive effects on health, including improving total cholesterol and low-density lipoprotein, or LDL, cholesterol; reducing blood glucose and insulin resistance; and by helping to regulate the hormone system that regulates blood pressure and fluid balance," Sun said.

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After posting yesterday "Probiotic Misconceptions", I was pleasantly surprised that today's NY Times had an article (by Jane Brody) raising similar concerns. What was good is that she wrote about supplements not being regulated. She also left out that probiotic beneficial organisms are found in more than the gut. A case in point being the sinuses - because healthy sinuses also have Lactobacillus sakei (according to the Abreu et al study of 2012), and which has been the basis for my family's successful kimchi treatment for sinusitis (see Sinusitis treatment link for the method). From the NY Times:

Probiotic Logic vs. Gut Feelings

The label on my bottle of Nature’s Bounty Advanced Probiotic 10 says it contains 10 probiotic strains and 20 billion live cultures in each two-capsule dose. The supplement provides “advanced support for digestive and intestinal health” and “healthy immune function.” I have no way to know if any of this is true. Like all over-the-counter dietary supplements, probiotics undergo no premarket screening for safety, effectiveness or even truth in packaging. 

To be sure, lay and scientific literature are filled with probiotic promise, and I am hardly the only consumer who has opted to hedge her bets. The global market for probiotic supplements and foods is expected to reach $32.6 billion this year,with a projected annual growth of 20 percent or more.

 Beneficial micro-organisms have since been shown to inhabit three main locations in the digestive tract: the stomach, the lower part of the small intestine and the large intestine. To better understand the current enthusiasm for enhancing the body’s supply of these micro-organisms, some definitions are needed.

■ Prebiotics are nondigestible carbohydrates that stimulate the growth and activity of beneficial micro-organisms (that is, probiotics) in the gut. They are found naturally in oats, wheat, some fruits and vegetables (bananas, onions, garlic, leeks, asparagus, soybeans, honey and artichokes), and in breast milk, and they are added to some infant formulas.

■ Probiotics are defined by the World Health Organization as “live micro-organisms which when administered in adequate amounts confer a health benefit on the host.” The ailments that probiotics are said to benefit range from infection-caused diarrhea, inflammatory bowel diseases and irritable bowel syndrome to asthma, allergy and Type 1 diabetes.

■ Synbiotics are a combination of prebiotics and probiotics. They are found in so-called functional foods like yogurt and kefir, fermented foods like pickles and some cheeses, and in some supplements.

That probiotic organisms are important to health is not questioned. As researchers at the Institute for Immunology at the University of California,Irvine have written intestinal micro-organisms play “an important role in the development of the gut immune system, digestion of food, production of short-chain fatty acids and essential vitamins, and resistance to colonization from pathogenic microorganisms.”

Dr. Walker has explained that probiotics enhance defensive action by the cells that line the gut. When a person takes antibiotics, especially the broad-spectrum antibiotics most often prescribed, many of these beneficial microbes are destroyed along with the disease-causing bacteria. Patients on antibiotics are often told to consume yogurt with active cultures to replenish the beneficial organisms.

In an extensive review of the evidence published in 2010 in the journal Pediatrics, an expert committee concluded that probiotics might limit the course of virus-caused diarrhea in otherwise healthy infants and children. But the committee said there was not sufficient evidence to justify routine use of probiotics to prevent rotavirus-caused diarrhea in child care centers. Nor did the committee endorse taking probiotics during pregnancy and nursing or giving them to infants to prevent allergic disorders in those at risk.

Only a small percentage of probiotic foods and supplements have the backing of peer-reviewed published research. They include Dannon’s Activia yogurt and DanActive drink and the supplements Culturelle and Align. Although kefir contains even more probiotic strains than yogurt, clinical studies have not shown it to be effective in preventing or treating infectious diarrhea.

The challenge in taking probiotics is to get the microbes past the stomach, where most are killed by gastric acid, said Robert Dunn, a biologist at North Carolina State University. Once in the intestines, they must compete effectively with the microbes already present.

Dr. Dunn, author of "The Wild Life of Our Bodies," says there is good reason to remain skeptical of probiotics. “There are hundreds of kinds of prebiotics and probiotics in stores,” he said. “As a consumer, it’s almost impossible to figure out what is best. What are the specific species in your intestines, and how will what you take compete with them?” Still, he added, taking them doesn’t seem harmful. 

There is growing evidence for the role of the appendix in restoring a healthful balance of microbes in the body. Though long considered an expendable, vestigial organ, the appendix is now being looked at as “a storehouse of good bacteria,” Dr. Dunn said. In a study of recovery rates from Clostridium difficile, which causes a severe form of infectious diarrhea, often following antibiotic therapy, patients whose appendixes had been removed were more likely to have a recurrent infection than those who still had appendixes.

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I keep overhearing misguided statements like these all the time: that somehow any and all probiotic (beneficial) bacteria offered for sale, whether in foods such as yogurt, or in probiotic capsules, are wonderful and beneficial, and will reseed your gut as well as do all sorts of miraculous things for your health. And while in reality, there are many, many bacterial species living in a healthy person's gut, it's the same few species that seem to be offered everywhere.

But if you look at the scientific research for even a few minutes, you realize that NO, we actually know very little about the health benefits of these bacteria species now in stores, and that all the claims out there don't have evidence backing them up. Perhaps taking megadoses of certain bacteria even has some negative effects. Yes, Lactobacillus species are generally considered beneficial by scientists. But even in the Lactobacillus family, there are many more types than the few now available in stores. For example. I can not find Lactobacillus sakei (which is found in kimchi and we use to successfully treat sinusitis - see Sinusitis Treatment link) in any store at this time.

Another problem is that sometimes you don't even get the desired bacteria that has been added to the food or cosmetic. For example, this occurs when some Lactobacillus or other bacteria are added to yogurt or some other food, but then the food is pasteurized, which kills off the bacteria. Duh...This is why I liked the following  opinion piece by Julianne Wyrick. From Scientific American:

Are probiotics helping you?

Consuming probiotics – also know as “good” bacteria – via supplements or yogurt has been popularized as a way to maintain gut health. While taking a daily dose of probiotics may not be harming you, it also may not be helping. The idea that every probiotic is good for every disease or condition is oversimplified, according to Catherine Lozupone, an assistant professor of medicine at the University of Colorado School of Medicine.

Lozupone spoke on a panel about the human microbiome, or the bacteria that reside in and on our bodies, that I attended at the Association of Health Care Journalists Conference last month. The panel touched on misconceptions related to probiotics, so I gave Lozupone a call post-conference to learn more.

One misconception Lozupone brought up was the idea that probiotic supplements should be used for “reseeding the good bacteria” missing in a person’s gut. Probiotic supplements often only contain a few species of bacteria, whereas a healthy gut generally has hundreds of species. In addition, the microbes that are abundant in a healthy gut are often different than those found in many supplements. A healthy gut is mostly composed of bacterial species that fall within a two different groups of bacteria: the phyla Bacteroidetes and Firmicutes. One group of bacteria commonly found in probiotics is known as Lactobacillus. While Lactobacillus is a type of Firmicute, it isn’t a type of Firmicute that is typically found in great abundance in a healthy adult gut, according to Lozupone. While Lactobacillus may be helpful for some people in some situations, the idea that everyone needs to repopulate their gut with this “good” bacteria is an overgeneralization.

“I think probiotics have a ton of potential, but different bacteria are going to do different things in different contexts,” Lozupone said. “This notion [of] ‘oh just reseed the good bacteria … they’re good for you’ is definitely very oversimplified.”

But while some general probiotic health claims are ahead of the research, studies do suggest that particular types of probiotic bacteria have potential for specific uses.

For example, Lozupone noted some rodent studies suggest certain microbes might mitigate certain effects of a high-fat diet, which could be helpful to treating obesity and associated health problems.

“There’s just lots of different contexts where the microbiome has been shown to be important,” Lozupone said. Going forward, researchers hope to not only find microbes that have health effects, but also understand why they have these effects. If you’re interested in keeping track of the current research into our body’s bacteria, keep your eye on the NIH’s Human Microbiome Project, an international effort to study the role of the body’s bacteria in our health.

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The study found real differences between organic and conventionally grown foods - organic foods have lower levels of pesticides, higher levels of antioxidants, and lower levels of cadmium. From NY Times:

Study of Organic Crops Finds Fewer Pesticides and More Antioxidants

Adding fuel to the debates over the merits of organic food, a comprehensive review of earlier studies found substantially higher levels of antioxidants and lower levels of pesticides in organic fruits, vegetables and grains compared with conventionally grown produce.

However, the full findings, to be published next week in the British Journal of Nutrition, stop short of claiming that eating organic produce will lead to better health. Still, the authors note that other studies have suggested some of the antioxidants have been linked to a lower risk of cancer and other diseases.

Organic farming, by and large, eliminates the use of conventional chemical fertilizers and pesticides. Those practices offer ecological benefits like healthier soils but produce less bountiful harvests. 

In the new study, an international team of scientists did not conduct any laboratory or field work of their own. Instead, they compiled a database from 343 previously published studies and performed a statistical procedure known as a meta-analysis, which attempts to ferret robust bits of information from studies of varying designs and quality.

Over all, organic crops contained 17 percent more antioxidants than conventionally grown crops, the new study found. For some classes of antioxidants, the difference was larger. A group of compounds known as flavanones, for example, were 69 percent higher in the organic produce. (At very high quantities, as in some supplements, some antioxidants have been shown to be harmful, but the levels in organic produce were not nearly that high.)

The researchers said they analyzed the data in several different ways, and each time the general results remained robust. Charles M. Benbrook, a professor at Washington State University and another author of the paper, said this analysis improved on earlier reviews, in part because it incorporated recent new studies.

The study also found that organically produced foods, particularly grains, contain lower levels of cadmium, a toxic metal that sometimes contaminates conventional fertilizers. Dr. Benbrook said the researchers were surprised by that finding; there was no difference in other toxic metals like mercury and lead.

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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 viruses. Viruses 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 harm. To 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.