From Birth, Our Microbes Become As Personal As A Fingerprint

Look in the mirror and you won't see your microbiome. But it's there with you from the day you are born. Over time, those bacteria, viruses and fungi multiply until they outnumber your own cells 10 to 1.

As babies, the microbes may teach our immune systems how to fight off bad bugs that make us sick and ignore things that aren't a threat.

We get our first dose of microbes from our mothers, both in the birth canal and in breast milk. Family members tend to have similar microbiomes.

"The mother's microbiome has actually poised itself over nine months to basically become the prime source of microbes to the infant," says , director of the at the National Institutes of Health.

But ultimately each person's microbiome seems to be unique, perhaps as personal as a fingerprint.

As the microbes colonize our bodies, they pick specialized real estate. The mouth, with all those moist nooks and crannies, is home to one of the most diverse habitats, like the Amazon jungle.

Wet places like our armpits are lush, too. But they have different microbes than those in the mouth.

The armpit microbes feast on nutrients in sweat, Proctor says, and produce antimicrobial compounds to protect the skin against harmful microbes.

Other body parts are like the Sahara Desert to your microbes. That forearm skin, for example, is dry — very dry. But even that driest habitat is brimming with microbes.

Feet have oily parts and dry parts, and it's those wet parts that the foot fungus just loves.

But the biggest habitat is the gut. It hosts the most complex and diverse group of microbes. Everything that microbes are doing elsewhere in the body, they're doing in the gut, in spades.

Diverse as these habitats are, the microbes on the various body parts communicate with each other and with our cells. Scientists have started eavesdropping on those conversations, and have started testing them as possible treatments for diseases like Crohn's, multiple sclerosis and asthma.

This research is all really new. No one knows for sure what most of our microbes are doing. But many scientists now think that if we're going to remain healthy, we have to maintain the health and well-being of the ecosystems for our microbes.

How A Change In Gut Microbes Can Affect Weight

The evidence just keeps mounting that the microbes in our digestive systems are a factor in the obesity epidemic.

A team of European researchers recently they'd found that obese people appeared to have less diverse microbes in their guts than did lean people. The research also showed that people with less diverse communities of gut microbes were more likely to be at risk for health problems associated with being overweight, including diabetes, heart disease and cancer.

Now, U.S. researchers are reporting the results of some intriguing experiments involving mice that got new gut microbes through transplants. The source: obese and lean human twins. (By using twins, the researchers were trying to eliminate any genetic variation that could influence the results.)

Biologist , of Washington University School of Medicine in St. Louis, and his colleagues removed bacteria from the guts of four pairs of human twins in which one was obese and the other was lean. The researchers then transplanted those microbes into the guts of lab mice who didn't have any of their own microbes.

The mice that got microbes from the obese twins gained more weight and accumulated more fat than those who got microbes from the lean twin, even when the mice ate identical diets, the researchers report in a in the journal Science.

Next, the scientists let the animals live together. And since eating each other's feces is a common habit among mice, they were soon exposed to each other's gut microbes. After 10 days, the researchers found that the mice with the obese microbes adopted the lean microbes and started to look healthier.

And, finally, the researchers showed that the animals were unable to be colonized by the lean microbes when they were fed diets aimed at simulating a typical unhealthful Western diet high in saturated fats and low in fiber.

"We now have a way of ... thinking about what features of our unhealthy diets we could transform in ways that would encourage bacteria to establish themselves in our guts and do the jobs needed to improve our well-being," Gordon said in a statement.

In an accompanying the report, and of the in Britain called the findings an "intriguing" step toward finding ways to fight obesity, including developing "relatively simple mixtures of bacteria for testing as anti-obesity therapeutics."

Staying Healthy May Mean Learning To Love Our Microbiomes

Not so long ago, most people thought that the only good microbe was a dead microbe.

But then scientists started to realize that even though some bugs can make us sick and even kill us, most don't.

In fact, in the past decade attitudes about the bacteria, fungi, viruses and other microbes living all over our bodies has almost completely turned around. Now scientists say that not only are those microbes often not harmful, we can't live without them.

"The vast majority of them are beneficial and actually essential to health," says , program director for the at the National Institutes of Health. The project is identifying microbes on key body parts, including the nose, gut, mouth and skin, in order to get a better sense of the microbes' role in human health.

This sea change began with a pretty simple realization.

"When you're looking in the mirror, what you're really looking at is there are 10 times more microbial cells than human cells," Proctor says. "In almost every measure you can think of, we're more microbial than human."

The horde of microbes is so vast that their genes swamp our genes. In fact, 99 percent of the genes contained in and on our bodies are microbial genes.

Scientists are getting a much broader idea of what microbes do for us. We've known for a long time that we depend on bacteria to digest food. But there's a growing realization that they're really like an 11th organ system. Proctor says, "You know, you have your lungs, you have your heart and, you know, you have your microbiome."

This week, scientists from NIH and research institutions are gathering in Bethesda, Md., to debate the in disease and human health, including obesity, behavior, heart disease and cancer.

Perhaps one of the most important things the microbiome does it to train the human immune system, starting at birth.

"It learns early on which microorganisms are friendly and how to recognize microorganisms that are not so friendly," says , an assistant professor of medicine at Stanford University School of Medicine who studies the relationships between microbes and humans.

Microbes influence how much energy we burn and how much fat we store. There is even evidence that the microbes in our guts send signals that can affect our minds. These signals may affect how the human brain develops, and our moods and behavior as adults.

People who live in places like the United States tend to have far less diverse microbiomes than people who live in less developed countries and take fewer antibiotics. That, some scientists think, could be a factor in human diseases.

"As organisms are being lost, a lot of diseases have just skyrocketed," says , who directs the human microbiome program at the NYU Langone Medical Center. He lists diabetes, celiac disease, asthma, food allergies, obesity and developmental disorders like autism as health problems that have become more common.

But many researchers caution that we're still a long way from knowing if the microbiome is involved in any of those diseases and conditions.

"Yes, the microbiome is important," says , a professor who studies genes, microbes and evolution at the University of California, Davis. "Yes, the microbiome differs between all sorts of health and disease states. But no, we don't know that the microbiome causes these health or disease states."

Even more important, Eisen says: we don't know how to fix a microbiome, even if we knew what was wrong with it.

Still, some doctors have already started performing microbe transplants. have been used to cure people with life-threatening infections with the bacterium Clostridium difficile. The patient's ailing gut bacteria is replaced with new colonies donated by a healthy person.

Getting good bacteria to drive out bad is also the idea behind probiotics, which are widely marketed as health supplements. But it's which of those microbes are helpful, and for whom. The same goes for , which serve as food for microbes.

This expanding view of the microbiome is changing how some people think about humans — not as individual entities but as what philosopher calls a "supraorganism."

"We're not just us by ourselves but a combination of us and them," Rhodes says. "And that makes us very much more a part of our environment as opposed to something freestanding and separate from our environment. Those are very radical changes in the way we see self-identity."

Rhodes, who is also a bioethicist at Mount Sinai Hospital in New York, says some people might find this idea shocking or gross. "But I think it's going to slowly seep into our culture and understanding of ourselves and change our understanding and consequently our behavior in important ways."

What Our Gut Microbes Say About Us

What if it's not just our genes or our lifestyle, exactly, that makes us skinny or fat, healthy or sick? What if it's also the makeup of the bacterial ecosystem that inhabits our gut?

A growing pile of is pointing us in that direction. Researchers in this hot new field describe the microbes in our gut as a vital organ that's as essential as our liver or kidneys. They're finding that this organ, which they call the "microbiome," varies greatly from person to person.

Some microbial communities are better than others at important nutrients, for instance. Also, this internal ecology is altered by the food that we eat, causing in the diet world.

But what constitutes a microbiome that's good for us, and how might you get one? So far, the researchers can't say.

The of these studies was published this week by the journal Nature. It compares the gut microbes of people who live in three very different parts of the world: The United States, the small African country of Malawi, and a remote Amazonian part of Venezuela.

The researchers, led by at the Washington University School of Medicine in St. Louis, found some across cultures and lifestyles. For instance, in each population, the makeup of the gut microbes changes dramatically as children grow older, whether they live in Amazonia or Philadelphia. In all three places, adults possess a more diverse collection of microbes than children.

But Gordon and his colleagues also found some intriguing differences, especially between people in the United States and those of the two other research sites. He found adults in the U.S. have a rather uniform collection of microbes living in them, compared to people in rural Malawi or the Amazon forests of Venezuela.

Gordon can only speculate about the reasons why — it could be because the U.S. uses more antibiotics, or perhaps because people in Malawi and Amazonia are exposed to more microbe-rich environments.

Gordon found some evidence that the microbiome of the gut may help a body out when there's a shortage of particular nutrients. Babies growing up in Malawi and in Venezuelan Amazonia both tended to have more microbes that can help to synthesize vitamin B2.

As Gordon puts it, "it is tempting to speculate" that these microbes may be helping to compensate for a lack of this vitamin in the babies' diets. These babies also had higher levels of microbes that are able to break down urea and use it to make essential amino acids. "This could be beneficial when protein isn't available in the diet," Gordon tellsThe Salt.

Sep 9, 2013 www.npr.org/.../from-birth-our-microbes-become-as-perso...

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