Robert Knight. Photo: James Duncan Davidson

The ancient Egyptians went to great pains to preserve the body for the afterlife. But there was one part of the body they didn’t bother with: the brain. Instead, they mashed it up, pulled it out of the nose and discarded it. Rob Knight wonders: Is there a part of our bodies that has just as much to do with who we are and  how we feel that we haven’t yet paid much attention to? Yes, he says. And it’s our gut.

Knight’s lab studies our microbial landscape, which he explains is “critical to a whole range of what makes people different.” For example, if you’re one of those people who gets attacked by mosquitos while no one else around the campfire gets a single bite, it’s probably because of the microbes on your skin. Meanwhile, microbes in the gut determine whether painkillers are toxic to your liver, or if a certain type of medication will work for heart disease. Our microbes help us digest food, they shape our immune system, and some evidence suggests that they might even affect our behavior.

Knight sequences the DNA of the microbial communities in different parts of the body and has turned terabytes of data from 250 healthy volunteers into readable maps. He shows us one, which looks like an upside-down pyramid composed of multicolored dots. In the top left corner are green dots that represent the oral microbial community, to the right are the blue dots of the skin community, just below are the pink dots of the vaginal community, and far below are brown dots that represent the fecal community. “The different regions of the body have very different microbes. Microbes from one person’s gut and mouth can be as different as what you find in the coral reef and the desert prairie,” says Knight. “A few feet in your human body makes more difference than hundreds of miles on earth.”

Human beings share 99.9% of DNA in common. But two people might only have  about 10% overlap in their microbes. It leads Knight to an interesting question: what comprises the human body? After all, we have 10 trillion human cells and 100 trillion microbial cells—and while we have 20,000 human genes, we have 2-20 million microbial genes. And while we leave traces of human DNA everywhere we go, we also leave traces of microbial DNA.

Our microbial communities are passed on during birth, when we’re coated in our mother’s vaginal microbes. This brings up an issue for children delivered via c-section, as the microbial communities passed to them look like skin, and this may be why they are at increased risk for allergies and asthma. “When my own daughter was delivered by emergency c-section, we took things into our own hands and made sure she was coated in vaginal microbes,” says Knight. “With one person, you don’t really have enough of a sample size. But she has not had a single ear infection.”

Knight shows a moving graph that charts a child developing its microbial landscape from day 1 through its second birthday. We see the four communities from the adult graph emerge—and then suddenly, there is a regression. Knight explains that this was when the child was given antibiotics for an ear infection. “This raises fundamental questions about what happens when we intervene at different stages in a child’s life,” he says. “It turns out that if you give children antibiotics in the first six months of life, they’re more likely to become obese later.”

Knight doesn’t mince words. “The three pounds of microbes that you carry around with you might be more important than every single gene you carry around in your genome,” he says. Microbes have been linked to heart disease, colon cancer and obesity in human beings and, in mice,  to multiple sclerosis, depression and autism. But, of course, it’s hard to tell if this is correlation or causation. Knight shares with us a line of experimentation raising mice in a germ-free environment without microbes of their own. Then, microbes are introduced to see what happens. If these mice are introduced to microbes from obese mice, they get fatter than they do than when introduced to microbes from lean mice. They appear to put on weight because they eat more than a regular mouse. “The implication is that microbes can affect mammalian behavior,” says Knight.

So what happens when a microbe-free mouse is introduced to microbes from an obese human being? That’s right—it begins to eat more and gain weight. This suggests that the strategy of introducing microbes from one person to another could potentially be used as a medical intervention. Knight explains how his team is studying children in Malawi with a type of malnutrition called “kwashiorkor” that causes them to lose 30% of their body mass in a week. Could introducing new microbes help them recover?

To further research, Knight’s lab has launched American Gut, a crowd-sourced science project that  8,000 people are participating in so far. “It lets you claim a place yourself on this microbial map,” Knight says. But beyond that, it can help scientists explore the idea that microbes could help cure diseases.

It’s a fascinating area of research. To underline just how much potential it has, Knight introduces us to C.diff, a disease that leaves people suffering from diarrhea 20 times a day. Some patients don’t respond to antibiotics, and his lab conducted a study on people who’d had this condition for at least two years. By transplanting fecal microbes from healthy individuals into these patients, there was an immediate change in their gut community. The disease was cured—in as little as a single day. And it didn’t come back.

We’re not yet to the point where techniques like this can be used clinically—much research lies ahead. But Knight and his co-workers would like to help us get there.

“We need to develop a microbial GPS,” he says, “to understand where we are, where we want to go and what we need to do to get there.”

The word ‘microbe’ sounds scary — we associate them with the flu, ebola, flesh-eating disease, you name it. But microbiologist Dr. Jonathan Eisen has given an illuminating TEDTalk that will make you put down the hand sanitizer. As Eisen explains, “We are covered in a cloud of microbes and these microbes actually do us good much of the time rather than killing us.”

Fun microbe fact: the average healthy adult has 10 times as many microbial cells as human cells. So what good things are these microbes doing for us? Here, some highlights.

1. Microbes play defense. The oodles of microbes that live on and inside us protect us from pathogens simply by taking up space. By occupying spots where nasties could get access to and thrive, good microbes keep us healthy. As Eisen explains, “It’s sort of like how having a nice ground cover around your house can prevent weeds from taking over.”

2. Microbes boost the immune system. Researchers at Loyola University demonstrated in a 2010 study how Bacillus, a rod-shaped bacteria found in the digestive tract, bind to immune system cells and stimulate them to divide and reproduce. The research suggests that, years down the road, those with weakened immune systems could be treated by introducing these bacterial spores into the system. These microbes could potentially even help the body fight cancerous tumors.

3. Microbes protect us from auto-immune diseases. In his TEDTalk, Eisen describes being diagnosed with Type 1 Diabetes as a teenager after “slowly wasting away until I looked like a famine victim with an unquenchable thirst.” Because microbes help train the immune system, if the microbiome is thrown out of whack, it can alter the body’s ability to differentiate between itself and foreign invaders. Recent research into Type 1 Diabetes reveals that a disturbance in the microbial community could trigger the disease, in which the body kills cells that produce insulin. In a 2009 study, researchers at Cornell University showed that introducing a benign strain of E. coli into diabetic mice set off a domino effect that led them to produce insulin. The work suggests that, someday, microbial yogurt could replace insulin shots for people with the disease. Microbial disturbances could be at the root of other auto-immune disorders too.

4. Microbes keep us slim. Microbes play an important role in our body shape by helping us digest and ferment foods, as well as by producing chemicals that shape our metabolic rates. Eisen explains, “It seems that disturbances in our microbial community may be one of the factors leading to an increase in obesity.”

5. Microbes detoxify and may even fight off stress. Just as humans breath in oxygen and release carbon dioxide, microbes in and on us take in toxins and spare us their dangerous effects. A recent study also shows that people feeling intense stress have much less diverse bacterial communities in the gut, suggesting that there is a not-yet-understood interplay between microbes and stress responses.

6. Microbes keep babies healthy. Recent studies have shown that babies born via caesarean section have very different microbiomes than those born the old-fashioned way. Why? Because during the birthing process, babies are colonized with the microbes of their mother, especially substances that aid in the digestion of milk. According to Science News, babies born via C-section are more likely to develop allergies and asthma than children born vaginally.
It’s clear that microbes have major implications for our health. And yet, much more research needs to be done to determine what different microbes do, and whether their disturbance causes ailments or is simply correlated to various health issues. To read more, head to Dr. Eisen’s blog or follow him on Twitter.