“Your microbiome is essentially another organ in your body,” says Shayne Morris, PhD, a molecular biologist at Systemic Formulas in Ogden, Utah.  “It helps you digest foods, create nutrients (such as vitamin K), combat pathogens (which can cause illness) and plays a critical role in the development of your immune system.”

That’s just the tip of the iceberg, though. Mounting evidence suggests your microbiome may play an important role in everything from autoimmune diseases to obesity. Scientists are continually uncovering new things about the microbiome and what it does.

In 2007, the National Institutes of Health announced the Human Microbiome Project, which collected and analyzed microbiome samples from healthy U.S. adults in an effort to determine what a “normal” human microbiome looks like. Since then, there’s been a whirlwind of activity.

“The microbiome is the new black,” says Jeff Leach, PhD, a microbiome researcher, founder of the Human Food Project, co-founder of American Gut, and author of Rewild (CreateSpace, 2015). “Everybody’s talking about the human microbiome because we now have the technology and computing power needed to better explore who’s in there and what they might be doing.”

The bugs inside you

“Not long ago, it was thought that everybody had different microbiomes, with each one of us being different, like a snowflake,” Leach says. “Now we know that when you gather microbiome data of several thousand people, as the American Gut Project has, you start to see some people with pretty similar microbiomes.”

To understand the variance from person to person, it’s helpful to understand a little bit about how bacteria are named. Bacteria, such as the ones you get in a probiotic supplement, are identified by their genus, species and strain, such as Lactobacillus (genus) acidophilus (species) LaVK2 (strain). Within each species, there are many different strains, which may have different benefits.

“In terms of bacteria genus, you are quite similar to those around you. However, when you look at abundance and narrow the microbiota to particular species and strains of bacteria, only about 15 percent will overlap with your neighbor’s,” Morris says. You would see even greater differences in microbiomes if you compared yourself to people in another country, due to differences in diet, lifestyle, environment and other factors.

Nurturing your microbiome

Your microbiome started developing while you were in your mother’s womb. “We no longer believe fetuses are sterile,” Morris says. “After you’re born, your microbiome changes dramatically until about age 3 as you go from breastfeeding to solid foods, then it starts to stabilize.”

“I highly recommend breastfeeding because there are more than 300 different polysaccharides (fermentable carbohydrates) in breast milk whose purpose is to directly nourish the microbiota, not to directly nourish the infant,” Morris says.

Antibiotics can disrupt the microbiome considerably. What you eat (or don’t eat) affects it a lot, too. In fact, so far studies show that diet, in comparison to other environmental factors, has the largest known impact on gut bacteria.

“Dietary fiber is food for microbes,” Leach says. “The human body cannot break down and digest dietary fiber, so it passes on to the colon where the bacteria harbor the genes that enable them to break down the fiber and turn it into energy.”

Feed them and they will come

Based on findings of the American Gut Project, Leach says people who eat a wide variety of plant foods have a greater diversity of bacteria in their gut than people who eat just a few plant species a week. The fiber in bell peppers is different from the fiber in baby spinach and different from the fiber in onions. That dietary fiber diversity is important to the health of your microbiome.

“Lactobacillus bacteria may prefer one type of fiber, but Bacteroides may prefer fiber from a different food,” Morris says. “As you diversify your diet with different plant foods, you diversify the bacteria that are now happy to stay with you. The diverse bacteria in turn help feed other bacteria. There’s this interplay between bacteria. If you omit certain foods and are no longer feeding the bacteria, they will eventually die off,” Morris says.

Unfortunately, diversity is one of the things we’ve lost in our Western lifestyle. “When we look at hunter-gatherers in East Africa, we find that they contain almost twice as much diversity in bacterial species as people in the United States,” Leach says.

Your bugs and your health

“Although the press has overhyped the microbiome as the new panacea that is going to save us all, there is pretty solid data that suggests microbes could play a potential causal role in a large number of ailments,” Leach says. “It could take years or decades to figure it all out though.”

Studies have associated disruptions in normal gut bacteria (dysbiosis) with obesity, diabetes, various inflammatory bowel diseases and autoimmune conditions, such as rheumatoid arthritis and type 1 diabetes.

When microbes munch on fermentable carbohydrates, including fiber and resistant starch, in your gut, they produce short chain fatty acids, primarily acetate, propionate, and butyrate, which may have far-reaching effects.

“Butyrate is very nourishing to the cells in your gut wall,” says Raphael Kellman, MD, author of The Microbiome Diet (De Capo Lifelong Books, 2015). Studies also suggest butyrate may help improve insulin sensitivity and blood sugar regulation. A significant amount of research (primarily from animals) also suggests short chain fatty acids may help in appetite control and managing your weight, such as by turning on the genes that drive fat breakdown.

A healthy microbiome also may help your memory, improve brain clarity, reduce your response to stress and improve your mood, Kellman says. Scientists are still uncovering how the microbiome could do all of this, such as by decreasing inflammation and supporting the production of brain chemicals including serotonin, a feel-good chemical.

About 90 percent of our serotonin is made in the gut, so if you have a healthy microbiome driving a healthy gut, you’re more likely to produce this important brain chemical.