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9 questions you were too grossed out to ask about the bacteria living on you

Hands under glow & tell machine in which microbes show up as white
Hands under glow & tell machine in which microbes show up as white
Photofusion/Universal Images Group/Getty Images

Your body is covered with microbes, inside and out. They're on your skin, in your ears, in your mouth, your gut, on your genitalia. It might sound gross, but it's perfectly normal — your bacterial cells outnumber your human cells by about ten to one.

And in recent decades, scientists have been learning much more about these microbes, even creating the Human Microbiome Project to categorize all the major microbial inhabitants that live on (and in) people. 

What researchers have discovered is that our bodies are essentially complex ecosystems of tiny living things. When these ecosystems are working normally, it helps us fight off harmful bacteria and aids in digestion. But scientists have also found that these microbial ecosystems can fall out of balance — and, some studies suggest, that could bring on a host of health problems, from obesity and eczema to allergies and possibly even some mental illnesses.

The science of the microbiome is still quite young — and, by and large, it's not yet ready to inform health or medical treatments. No one can tell you if a certain microbe really causes obesity or if you should be eating a special diet to influence your inner zoo. But the possibilities are certainly intriguing.

1) What is the microbiome?

The human microbiome is the sum total of all the microbes that live in and on the human body, including viruses, fungi, archaea, and bacteria. (The word can also refer to the sequences of these species' genetic material.)

A lot of work on the human microbiome focuses on bacteria. Non-humans have microbiomes, too, including other primates, your pet dog, amphibians, soil, plants, you name it. The world is covered in microscopic creatures.

Microbiome body

Various groups of bacteria in locations around the human body. (Darryl Leja, NHGRI via Wikimedia Commons)

2) Am I wrong to not want trillions of microbes living on my body? This sounds bad.

It's not bad to have trillions of microbes living in and on you. In fact, it's perfectly healthy.

3) How did microbes get there in the first place?

A fetus in the womb is fairly sterile. But when babies are born, they pick up all sorts of microbes from either their mother's vagina or from the operating room, in the case of C-sections.

As it turns out, the method of delivery actually makes a difference. Studies suggest that children delivered by vaginal birth have a lower incidence of asthma and obesity, which some researchers think may be related to picking up better microbes while being born.

From then on, children likely get microbes from all over the place — from family members, from surfaces, from dirt, from pets, from food and what kinds of foods they eat.

A child's gut ecosystem is in a state of fairly flexible development until about age two or three, when it becomes more stable. That means that events in those early years could have big consequences for who's living in your gut decades later.

4) So what are these microbes doing to me?

It might be better to think of it as what are they doing for you.

Microbial ecosystems play a helpful role in many parts of the body. Beneficial bacteria are thought to crowd out more harmful bacteria (such as Clostridium difficile) that could make you really sick.

They also play a role in your digestive process, helping break down molecules such as complex carbohydrates so that your body can use them for energy. And some microbes produce useful byproducts, such as vitamin B12, which humans cannot produce themselves.

Beyond that, it's difficult to say. Researchers are still exploring possible links between certain microbes and various health conditions, but solid causal evidence in humans is hard to come by right now. Some of the more suggestive studies, including some big ones about obesity and anxiety, were actually performed in lab mice, which might not translate to humans.

5) Does everyone have the same microbes?

No. And that's why researchers are so interested in exploring possible connections between the microbiome and human health. Your microbiome depends on who you've been around (families have more in common than strangers), what you eat, and more.

For instance: One recent study found that simply changing a diet altered the proportions and identities of microbiomes in the gut within days. Ed Yong has a great profile of this work over at Not Exactly Rocket Science. The results suggest that, even in adults, the gut microbial ecosystem still has some impressive flexibility.

Culture also makes a difference. Many Japanese people have strain of gut bacteria that digests seaweed more easily — a strain that people in other counties tend to lack.

Likewise, in the few communities that have been studied so far, people in westernized cultures have tended to have gut communities that are different from those living other lifestyles. Studies have shown that the gut microbes of indigenous people in Venezuela more resembles those of villagers in Malawi than of Americans. This might mean that westernized lifestyles, including diet and antibiotic use, have changed our microbiomes — which might explain some of the disparities in rates of things like obesity or asthma.

Still, many scientists remain cautious about reading too much into these differences. "The implications of those changes are not understood," says Catherine Lozupone, who studies human microbiomes at the University of Colorado at Denver. Many scientists are working to figure it out, but it's a very large project.

Not only that, but a person's microbes vary from body part to body part and even from day to day. Taking a course of antibiotics or getting sick can change a person's gut microbiome — even after the person gets better.

Traveling abroad or getting sick can change your gut microbiome — and possibly for a very long time:

Microbiome perturbations

Different colors represent different groups of related gut bacteria. Subject A traveled to Southeast Asia and experienced some diarrhea. Subject B got food poisoning and recovered without using antibiotics. H/t Carl Zimmer. (David, LA et al. Genome Biology 2014, 15:R89)

6) How do scientists map all the microbes?

Two major technologies have come together to allow the current boom in microbiome research.

The first is genetic sequencing, which has gotten faster and less expensive (to the point that a commercial lab will happily sequence your gut microbiome for just $89). The second is increased computing speed, which can help scientists sort through the large, jumbled data sets that such sequencing produces. (These technologies have enabled all sorts of genetic research, and they're helpful with microbes, too.)

One major research approach has been simply trying to catalogue the microbes from healthy people and see how they vary between people, between cultures, between diets, and between people who are healthy and who are ill.

This type of research can provide correlations between certain microbes and certain health conditions, but it's much harder to prove causation. For example, did a person become obese because of his gut bacteria, or did his gut bacteria simply change because of poor diet, which also caused his obesity? Or did poor diet change the gut bacteria, which then compounded his obesity? This isn't always easy to disentangle.

One way researchers try to pin down causal links is to study "germ-free" mice. These mice are raised in sterile environments and so have no bacteria on their own. Researchers can then give them mouse or human bacteria and see what happens. Experiments like these have shown that the gut bacteria from an obese person, combined with a poor diet, can make a mouse obese. Researchers are also doing similar studies to explore other health problems, including anxiety.

Although scientists know that thousands of microbial species are living on people, they don't know a lot about what all of them are actually doing to us. So researchers also grow these microbes in the laboratory, alone or in small communities. From there, they can try to study what they do and how.

7) How can I map my own microbiome?

American Gut Project microbiome

Author Michael Pollan's gut microbiome. Pollan also wrote a story about it for The New York Times Magazine. (American Gut Project)

Unless you have a laboratory, you're going to need some help. Two projects out there, American Gut and uBiome, will sequence a feces sample or two for you for about $100.

But there's a huge caveat: because this is a very young scientific field, the techniques can be unreliable. So results may vary. When science writer Tina Hesman Saey sent out similar samples to both places, she got different analyses back. "The results didn’t match at all," she wrote in Science News . "I’ve had my microbiome sequenced twice, but I still don’t really know what’s in there."

Getting a list of your microbial residents can be fun (and can support ongoing scientific efforts), but it won't necessarily tell you what it means. So it's good to keep expectations in check.

8) So will probiotics make my bacteria healthier?

It's unclear. There are a lot of probiotic products out there, but very few have been rigorously demonstrated to be directly beneficial for human health.

Justin Sonnenburg, a biologist who studies the human microbiome at Stanford University, says that people should be wary of supplements claiming to be probiotic because their claims and contents aren't tightly regulated.

But Sonnenburg does recommends that you "take care of your gut microbes" through steps that he takes himself: eating lots of varied dietary fiber (which some gut bacteria like to eat), consuming fermented foods (which contain microbes), and only using antibiotics when absolutely necessary. He also recommends breast-feeding children to help recruit helpful microbes into their guts when they're young, which might affect them for decades to come. To be sure, Sonnenburg notes that there isn't necessarily solid medical evidence that these things help — but they're also unlikely to hurt. "The field is still in a really early stage," he says. "This is an evolving story."

9) Will understanding the microbiome help cure a lot of diseases?

Maybe. It's worth emphasizing again that a lot of microbiome research is interesting exploratory science — but it's not even close to being useful for medical treatments. So only time will tell what sort of an effect this research will have.

There is, however, one microbe-based medical treatment that does seem to be getting fairly good results: fecal transplants. Here's how it works. Sometimes a strong dose of antibiotics can wipe out healthy bacteria in a person's gut, which then allows the harmful bacteria Clostridium difficile to flourish (and kill some 14,000 Americans a year). By transplanting feces from a healthy person into the patient's intestines, doctors can restore a bacterial balance, which controls C. difficile.

But it's worth noting that a fecal transplant is an extremely blunt instrument. Doctors are essentially transferring hundreds of microbial species from one person to another with the hope that some will help (and we don't know exactly which ones they are). That just underscores how much there is to learn about the microbiome.