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 Lita Proctor, program director for the Human Microbiome Project 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 microbiome's role 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 David Relman, 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 Martin Blaser, 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 Jonathan Eisen, 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. Fecal 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 still unclear which of those microbes are helpful, and for whom. The same goes for prebiotics, 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 Rosamond Rhodes 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."