Understanding Your Microbiome: Definition and Significance

Your microbiome is all the microbes (e.g., bacteria, fungi, viruses) that live naturally in your body—including microbe communities in your gut, on your skin, and in your nasal cavities. The gut microbiome seems to play a particularly important role in health.

Your gut microbiome is the community of microbes in your gastrointestinal (GI) system. This environment of trillions of microorganisms influences your health in multiple ways, including supporting digestion, regulating your immune system, and affecting how your central nervous system (CNS) functions.

The balance of the microbiome is linked to disease development and prevention. Researchers are discovering more and more that what happens in your gut can greatly affect your overall health and wellness.

Your gut microbiome is responsible for maintaining a balance of trillions of different bacteria, fungi, viruses, and parasites that help support digestion, gut health, and more. It’s located in your gastrointestinal (or GI) tract, which includes the stomach, small intestine, and large intestine (colon).

Your gut microbiome interacts with multiple bodily functions and systems, including:

• Digestive system: Assists with breaking down nutrients, metabolizing bile (liquid produced by your liver, which breaks down fat in your small intestine), producing fatty acids that support the gut barrier (layers that protect your gut from outside pathogens like bacteria), and reducing inflammation
• Immune system: A helpful partner in fighting infection-causing microorganisms
• Central nervous system (CNS): Influences the network of nerves in your GI tract that send chemical signals to your brain

Each person’s microbiome is unique. Various factors can affect the environment of microorganisms in the gut.

For example, intestinal motility—the automatic movement of food through the GI system—plays a role in the types, amounts, and functions of microorganisms in the gut microbiome.

Genetics and Early Life Experiences

Genetics influences the amounts and types of microorganisms found in the gut microbiome. Research shows that families tend to have similar microbiome communities. However, experts haven’t identified any particular genes linked to microbiome composition.

Circumstances in early life and childhood may influence the gut microbiome. For example, a vaginal delivery provides exposure to bacteria at birth, while breastfeeding introduces bacteria to the microbiome. These two factors can ultimately affect how the microbiome develops and remains throughout life.

Diet and Medications

Diet is another important factor. Studies show that eating a fiber-rich diet and fermented foods (like yogurt and sauerkraut) can positively affect the microbiome. Consuming foods high in fat may reduce the variety of microorganisms in this environment.

Certain medications can also affect the microbiome. Taking antibiotics to fight off a bacterial infection reduces the “good” and “bad” bacteria in your gut. Metformin, sometimes used in type 2 diabetes treatment, might also affect the microbiome. Experts are still studying exactly how this happens and the relationship between type 2 diabetes and gut health.

The gut microbiome is linked to a variety of different health conditions, many related related to the GI system, including:

• Irritable bowel syndrome (IBS): A chronic (long-term) inflammatory condition that includes symptom flare-ups like diarrhea and constipation
• Inflammatory bowel disease (IBD): Chronic inflammation in the GI tract, including the conditions Crohn’s disease and ulcerative colitis (UC)
• Colorectal cancer: Colon or rectum (lowest part of the colon) cancer
• Type 2 diabetes: A condition that develops when your body can’t use insulin effectively

Symptoms of Gut Dysbiosis

Gut dysbiosis is an imbalance of the gut microbiome. This could mean an overgrowth of “bad” bacteria or not enough “good” bacteria. It may increase your risk of developing another GI condition, like IBS.

Symptoms of gut dysbiosis include:

Gut microbiome testing—also known as gut health testing—can help provide a better picture of what’s happening in your gut. While gut microbiome testing isn’t meant to identify each individual bacteria or microorganism that’s present in the gut, it can offer a more generalized overview of the following:

• The potential balance of “good” and “bad” bacteria in your gut
• Any specific harmful bacteria or other microorganism that may be causing infection or illness
• Digestion and gut lining health

An official medical diagnosis should be made by a healthcare provider. If you’ve been experiencing bothersome digestive symptoms like bloating, gas, diarrhea, or constipation, a healthcare provider may order certain tests to help identify an underlying cause. Testing options include:

• A stool test: To help diagnose infections, GI conditions, and colon cancer
• A urine test: To check for specific acids that certain gut bacteria produce
• A hydrogen breath test: To measure the amount of hydrogen in your breath, which could indicate a bacterial imbalance like helicobacter pylori (H. pylori) infection
• Diagnostic procedures: Tests like an endoscopy (special imaging performed through the stomach) or a colonoscopy (imaging performed through the colon) to better visualize the gut

The gut microbiome is fluid and can fluctuate. One gut microbiome test may not provide a full picture of a specific microorganism imbalance, as results could differ days or weeks later depending on factors like what you recently ate and whether you’re fighting an illness or infection. 

Research supports important connections between a healthy gut microbiome and overall health. Experts continue to explore how addressing the microbiome can help treat disease and improve health.

For example, scientists have been studying how keeping your microbiome healthy through diet—like high-fiber foods—can help prevent health conditions like hypertension (high blood pressure) and cancer. Probiotics may also positively interact with the gut microbiome to encourage healing, especially after antibiotic use.

Another study area includes clarifying the microbiome differences in people with certain health conditions so that disease may be diagnosed before it develops.

Other areas of research include how environmental factors like the following affect microbiome and overall health:

• Air pollution
• Antimicrobials (e.g., in drinking water)
• Diet choices like artificial sweeteners
• Stress
• Flame retardants
• Pesticides

Current knowledge about the microbiome is already used in certain types of treatment. The U.S. Food and Drug Administration (FDA) recently approved the first fecal microbiota therapy for recurrent Clostridioides difficile (C. diff) infections. This involves transferring a healthy human stool to another person via a capsule or enema. It’s a promising treatment for potentially life-threatening C. diff infections that cause GI symptoms.

The gut microbiome is the environment of microorganisms that exist in the gastrointestinal (GI) system. Multiple factors can influence the microbiome, including genetics, diet, lifestyle, and more. Research shows that this balance of “good” and “bad” bacteria, virus, and fungi contributes not only to digestive health, but to a variety of different aspects of overall health.

Experts are currently looking into how the gut microbiome may be positively manipulated to help treat and prevent disease.