(07-05) 15:12 PDT STANFORD -- In the search for new life, scientists have studied the depths of the ocean and the lips of steaming volcanoes. They've looked on Mars and the moons of Jupiter, and even planets beyond this solar system.

Dr. David Relman went searching inside his own mouth. On a routine dental visit in 1998, Relman, a Stanford infectious disease expert, brought along a test tube. When the dentist scraped the plaque off his teeth, Relman asked for a sample of it.

What he discovered back in his lab was, at the time, shocking. Using relatively new DNA sequencing technology, he found 31 bacteria that had never been seen before.

"As a clinician, I can tell you, my colleagues were not looking for new things to worry about from the microbial world," Relman said. "Some of them believed that sure, there may be some really weird microbes in soil or in the ocean, but the human body is something we understand.

"Of course, that was wrong."

So very wrong. Last month, an international team of scientists published the results of the first-ever DNA sequencing of the entire human microbiome - the colonies of bacteria that live in and on our bodies, sometimes working against us when we're sick, but mostly working with us in harmless and even favorable ways.

Truckload of bacteria

The results of their sequencing are staggering. The human body carries more than 100 trillion bacteria - up to five pounds of the tiny single-celled organisms. The mouth alone has several hundred species of bacteria. Each tooth is its own ecosystem.

Together, all of the bacteria in the body would be the size of a large liver, and in many ways, scientists say, the microbiome behaves as another organ in the human body.

Each of our bodies has its own unique microbiome, cultivated from birth and built from our genes and our diet, nurtured by our exposure to a family dog or cat, by how much dirt we ate out of the sandbox and the antibiotics we've taken for ear infections or strep throat.

Bacteria, for more than a hundred years seen only as a bane of human existence - the cause of fatal illnesses and gut-cramping food poisoning - have, over the past decade, increasingly come to be seen as benevolent life partners. Most people will carry the same basic set of bacteria over their lifetime, and while some microbes may cause gingivitis, others may be actively working to keep our gums healthy.

The research released last month involved the sequencing of the microbial communities of 242 healthy adults, focusing on colonies found on the skin and in the mouth, nose, gut and vagina. Already, scientists are expanding on that research - studying the microbiomes of infants, and of people with particular diseases.

The next frontier

Understanding the microbiome goes beyond the curiosity the leads researchers to explore the unknown. It could someday explain the modern epidemics of obesity, asthma and allergies. It could reveal new treatments for gluten intolerance or drug-resistant staph infections, or to aid in weight loss.

It could, some scientists say, be the next frontier of medicine.

"It's almost like space exploration or understanding the oceans," said Dr. Julie Parsonnet, a Stanford epidemiologist who refers to her peers as "microbonauts." "It's very complicated, it's very unknown, it's very hidden. We're still scratching the surface."

Yet, their research of a healthy microbiome is producing an overwhelming amount of data - just the 100-plus trillion bacteria in a single human being is too much for one computer to analyze. Scientists still want to map the bacteria in sick humans, or humans who have taken a strong course of antibiotics that has altered their bacterial community.

And scientists like Relman want to dig deeper - studying the way bacteria in the body communicate with one another and with their hosts. That communication happens via molecules sent constantly from bacteria to human cells, and each of those molecules could hold the clue to a new drug for cancer or staph infections.

Killer molecule

In fact, our best disease-fighting drugs - antibiotics - are basically communication molecules with instructions to kill bacteria. So it's a little ironic, and a relatively new finding, that some bacteria, including bacteria in our own bodies, produce antibiotics. For more than a century, scientists have been traveling the world looking for new bacteria to produce new antibiotic molecules, but they might now want to search much closer to home.

"The bacteria inside us ... are synthesizing hundreds of molecules in our mouth or our gut or our skin," said Michael Fischbach, a UCSF bioengineer. "We shouldn't be afraid of that. We should learn more about it."

While drug discovery is one possible long-term benefit from the study of the microbiome, the more immediate hope is to learn how humans can somehow work with their own bacterial colonies to cure or prevent chronic disease, or just maintain good health.

Over-the-counter probiotics already are being sold and promoted for bacterial health. Probiotics are, essentially, good bacteria that are mostly associated with improving digestion but may have other benefits. Many people use probiotics to, in theory, replace some of the healthy bacteria that may be killed by a course of antibiotics.

Study on probiotics is limited, and many microbiologists question whether they're helpful. On the other hand, they're probably not harmful, they say. The same is true for diets thought to promote healthy bacterial colonies.

But despite a notable lack of evidence on the relative benefits of tinkering with the microbiome, many scientists experiment with their own bodies anyway, in hopes of building a welcome environment to entice, and retain, the most helpful bacteria.

Janet Jansson, a microbiologist at Lawrence Berkeley National Laboratory who was part of the national human microbiome project, isn't necessarily interested in sequencing her own bacterial biome.

"But the more I go to these microbiome conferences, the more I have manipulated my own diet," Jansson said. "There are some fairly easy things you can do to keep the microorganisms in your gut in a certain state. They aren't very drastic things to do, just minor modifications of lifestyle."

Bacteria's many roles

At Stanford, Parsonnet is studying, among other things, how the microbiome might influence weight gain and obesity. Some scientists theorize that modern humans, over decades of adopting new diets, have altered their microbiomes, which in turn has altered the way they digest food or process the energy from it, or even changed the foods they crave.

At least one parasite - toxoplasmosis gondii - has been shown to affect behavior. The parasite reproduces only in cats, and studies have shown that when mice or rats are infected with it, the parasite makes them less afraid of cats, and they are, therefore, more likely to be eaten by them.

If that parasite can influence behavior, who's to say other microbes aren't having similar, if more subtle and less fatal, effects in humans? It's unlikely that modern humans are going to pick up a strain of bacteria that makes cauliflower as appealing as french fries, said Stanford microbiologist Les Dethlefsen.

But lactose intolerance, for starters, is thought to be caused by bacteria in the gut that, when they consume lactose, release large amounts of gas that can make people uncomfortable.

"I tend to take quite seriously people's anecdotal experiences of 'I eat this and this happens so I avoid this food,' " Dethlefsen said.

Like many of his colleagues in microbiology, Dethlefsen has a pretty intense interest in his own gut and the rest of his microbiome. Many microbiologists say they're much more likely to avoid antibiotics, for fear of upsetting their balance of healthy bacteria.

Dethlefsen tries to eat more fruits and vegetables. Jansson has been experimenting with "resistant starch," which is a type of food that resists digestion and is therefore more likely to reach bacteria and nurture them.

Fischbach at UCSF is perhaps facing the most difficult challenge: caring for his days-old daughter and nurturing her infant microbiome. He's in the tough position of having both too much and not nearly enough information.

"My wife and I have tried to pledge to each other that this is going to be our baby, not our experimental subject," Fischbach said with a laugh. "At the same time, my thinking is influenced by the things going on around me. The cast of characters in her is changing dramatically week to week, day to day. I do wonder, where are most of the bacteria that she's got in the gut coming from?"