The Microbiome of Your Gut

Part of The Secret World Inside You exhibition. 

Millions of microbes enter your body at every meal. Indeed, after your skin, the digestive system is the main place where your body comes in contact with microbes.

Researchers culture some of the microbes that live in the human gut to learn more about them. Courtesy of Pacific Northwest National Laboratory

Researchers culture some of the microbes that live in the human gut to learn more about them.

Courtesy of Pacific Northwest National Laboratory


But unlike your skin, your digestive system is a warm, sheltered space—and it’s filled with food, making it the perfect spot for microbes. So it’s no surprise that the vast majority of your body’s microbiome is inside your digestive tract.

The microbiome of your gut doesn’t just effect what happens there. New research shows that the state of your gut can impact your moods and behavior. Mood-affecting chemicals like serotonin are produced in large quantities in the gut, and changing the gut microbiome in mice has been shown to affect their behavior and anxiety levels.

The Mouth

Bacteria in the genus Prevotella have numerous homes in the microbiome, including the mouth, where they can cause tooth decay. © AMNH/B. Peterson

Bacteria in the genus Prevotella have numerous homes in the microbiome, including the mouth, where they can cause tooth decay.

© AMNH/B. Peterson


Your mouth is where food—and microbes—enter your digestive system. Some bacteria go no farther. You probably have 100 to 200 species living in your mouth right now.

Most either do you no harm, or actively protect you from infection. But if ecological conditions favor them, other microbes can cause tooth decay, bad breath and gum disease. 

Hunger, Immunity and the Microbiome

While it can cause ulcers, researchers believe that Helicobacter pylori may also play a crucial role in human health. © AMNH/B. Peterson

While it can cause ulcers, researchers believe that Helicobacter pylori may also play a crucial role in human health.

© AMNH/B. Peterson


For a long time, the bacterium H. pylori was found in human gut microbiomes around the world. When a connection between the bacterium and ulcers was made in the mid-20th century, though, efforts were made to prevent this painful condition by wiping out the bacterium that caused it. Now, less than 10% of children in the U.S. carry this bacterium. 

New research, though, suggests that H. pylori may play a key role in human health. It modulates the immune system to reduce the risk of allergies and asthma, prevents esophageal cancer and gastric reflux disease, and even helps regulate appetite, with experiments showing that the removal of this bacterium is associated with weight gain..

The Digestive Tract 

Digestion—the process of turning food into nutrients your body can use—involves a lot of work, mostly at the molecular level. Fortunately, you have a lot of help.

Bacteria in your body turn undigested fiber into useful chemicals. They also produce many other molecules your body needs, using raw materials from your food.

Used to produce foods such as yogurt and pickles, Lactobacillus bacteria also  appear many places in the microbiome, including the digestive tract. © AMNH/B. Peterson

Used to produce foods such as yogurt and pickles, Lactobacillus bacteria also  appear many places in the microbiome, including the digestive tract.

© AMNH/B. Peterson


Your digestive tract is home to around 100 trillion bacteria—more than all the stars in the Milky Way galaxy. But the digestive system is a big place, and not every part of it is valuable microbial real estate.

The stomach for instance, hosts very few microbes, while the small intestine (where food is digested) has some microbes and the large intestine (where food ferments after digestion) is home to the majority of those trillions of microbes.

Diet Diversity 

The old saying ‘you are what you eat’ holds true for the microbiome of your gut. Diet can have a serious impact on the population of microbes in your stomach. For instance, people in hunter-gatherer cultures who eat traditional diets tend to have much more diverse microbiomes than those on less diverse Western diets which are heavy on processed food.

Layers of Life

One way to visualize the different neighborhoods in the digestive system is with a Winogradsky column. Named after a famed microbiologist, a Winogradsky column provides a place for different types of bacteria to grow and a window through which you can view them. 

To learn how to build your own Winogradsky column at home, click on the image below. 

©AMNH/5W Infographics 


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