This 2004 electron microscope image made available by the Centers for Disease Control and Prevention showed a cluster of Clostridium difficile bacteria. The intestinal bug flourishes in the gut after antibiotics kill off other bacteria and causes diarrhea. Janice Carr | AP

Dan Knights works on a growing new frontier in medicine: the microbiome. He's on a team of researchers at the University of Minnesota trying to better understand the microbes living in and on your body and the complex system in which they function.

The latest research shows your gut microbiome has a profound connection to a number of diseases and issues facing humans today: Diabetes, Crohn's disease, obesity, asthma, allergies and other autoimmune diseases. While scientists have believed these bugs played a role in our overall health, it was only recently that they were able to get an in-depth look.

The major turning point came after scientists sequenced the human genome at the turn of the millennium, Knights said.

"The reason there was this big shift is that most of those bugs don't really grow easily in the lab," he said. "Prior to the DNA sequencing, there was no way to study them."

For example, we know a lot about e.coli because it grows well in a lab setting. But it only exists in about a tenth of a percent of most people's guts.

So what do researchers know about the bugs living in us — and what are they still trying to figure out? Knights helped break down the data.

What we know about the microbiome

Want to understand the basics? These videos give a good overview:

The bacterial cell population in an average human outnumbers human cells 3-to-1

Your microbiome weighs approximately 2 to 3 pounds, Knights said. That would fill about three pints. A normal human microbiome includes about 1,000 species.

You get a lot of your microbes from your mother in the early stages of life

From a recent U of M study in the scientific journal Cell Host & Microbe:

Although the GI tract of a healthy infant is generally considered to be sterile before birth, recent work suggests that initial colonization may take place in-utero. Hours after birth, microorganisms from the mother's vaginal, fecal, and/or skin microbiome and the environment are important colonizers of the infant gut, with actual contributions depending on mode of delivery. Several other factors including prematurity, infant diet (breast milk or formula), hygiene, and use of antibiotics will ultimately impact the composition of the infant gut microbiome.

Infants born vaginally have a microbiome that resembles their mother's vaginal and intestinal microbe population — and infants born by cesarean section have a microbiome that resembles the microbes found on their mother's skin.

Women breastfeed their babies at the Hirshhorn Museum in Washington on February 12, 2011 during a "nurse-in." NICHOLAS KAMM/AFP/Getty Images

Researchers can also predict an infant's age within 1.3 months based on the maturity of gut bacteria. Knights said this could be used in the future to measure the health of infants compared to normal gut flora development. The infant gut continues to develop and change over the first three years of life before it resembles that of an adult.

Breast milk is a pre-packaged microbe delivery system

In addition to nutrients, vitamins and antibodies, breast milk also provides bacteria to help populate the infant's gut. It also provides specific foods needed for the bacteria to survive.

From the American Society of Microbiology:

Breast milk also contains a number of complex carbohydrates (oligosaccharides) and glycosolated proteins that actually cannot be digested by the infant. However, they are readily consumed by bacteria of the Bifidobacterium species. Bifidobacteria are the dominant species in the infant microbiome and are thought to play a role in coating the intestinal surface and preventing the attachment of pathogens. Thus, breast milk contains both probiotics (beneficial microbes) and prebiotics (compounds that support the growth and establishment of beneficial microbes).

Antibiotics during infancy have long-term effects on your gut diversity and are associated with chronic conditions in adulthood

Broad-spectrum antibiotics are designed to wipe out bacteria in the body, including good strains. This is a drastic shift for a gut to handle and researchers believe it has long-term health consequences, particularly when it occurs early in life. While the gut can rebound, the recovery period or incomplete recovery can be a problem, Knights said.

"Previous studies showed links between antibiotic use and unbalanced gut bacteria, and others showed links between unbalanced gut bacteria and adult disease, Knights said. "Over the past year we synthesized hundreds of studies and found evidence of strong correlations between antibiotic use, changes in gut bacteria, and disease in adulthood."

Your microbiome diversity is different from others and changes based on where you live, what you eat, how you live

"We know there's been dramatic loss of diversity in the modern human microbiome as compared to indigenous populations," Knights said. "We know there's a big shift comparing non-westernized to westernized populations."

Researchers are studying the microbiome diversity of immigrants to westernized countries and looking at changes in lifestyle, including diet changes, stress and exposure to antibiotics.

University of Minnesota post doctorate fellow Matt Hamilton displays a sample of fecal bacteria at the St. Paul, Minn. campus Nov. 14, 2012. The fecal matter is donated and used to treat patients with Clostridium difficile, an intestinal disease that is caused when a person's gut flora is eliminated by antibiotics. Jeffrey Thompson | MPR Photo file

Some other things that change your gut diversity: You share microbes with the people you live with. Your guts are even more alike if you have a dog that helps pass those microbes between family members.

Fecal transplants cure a particularly strong infection by changing the makeup of your gut

The University of Minnesota's Alexander Khoruts is one of the leaders in this procedure. Doctors transplant the stool of a healthy individual into someone suffering from clostridium difficile, an infection that kills 14,000 people in the United States every year.

More from MPR News:

Doctors say fecal transplants could allow patients to more quickly develop their own natural defenses against clostridium difficile, an infection that kills 14,000 people in the United States each year, according to the U.S. Centers for Disease Control and Prevention. The antibiotic-resistant bacteria, which many contract in hospitals, typically are treated with strong drugs. But using the antibiotics can be a double-edged sword, as the drugs also destroy good bacteria that normally keep harmful bacteria in check. If too much good bacteria are lost, the disease can flare up again soon after antibiotic treatment is stopped.

Your gut health affects your whole body

Check out this graphic for some examples, including depression, autism and schizophrenia.

What we don't know about the microbiome

Is it correlation or causation?

"We know the microbiome is associated with all of these diseases, but in most of the cases we don't know the mechanism and we don't know the causation," Knights said.

There's an intense interest in making those causal links, Knight said, which means figuring out which features of the microbiome matter and how to use that information to prevent disease and infection. In the future, doctors could potentially give you a bacteria cocktail to help a particular ailment, Knights said.

You can have your microbiome analyzed, but it's not prescriptive

Projects like American Gut will send you a report of your gut population, but doctors won't be able to tell you much from it, Knights said.

In collaboration with Khoruts and Michael Sadowsky at the University of Minnesota, Knights' lab is currently developing a clinical test to tell you whether your microbiome is normal.

Researchers can't say exactly what makes a microbiome healthy for you

The success rate of fecal transplants has people hoping it can be used as a treatment for other problems, but Knights said you shouldn't experiment on yourself. Researchers are still working to find out what makes healthy transplant material and how it needs to fit within your current microbiome.

For example, if you get the bugs to cure your c-diff infection, could those bugs cause you to become obese? Could another person's microbiome used to treat your Crohn's Disease give you an infection?

How sterile should our lives be? That's still up for debate

Antibiotics have obviously been a major development for humans to battle serious infections, but there's a trade-off, Knights said. Researchers are still trying to find the balance between sterile environments and ways for humans to come in contact with good bacteria.

Knights said he has taken some actions in his life to reflect what he knows about gut health: He is cautious about antibiotic use in his children and doesn't worry as much about them sharing food or playing in the dirt.