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What Is the Gut Microbiome?

What Is the Gut Microbiome?
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Updated on July 29, 2026
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Your body harbors communities of bacteria and other microorganisms both inside and on your skin. These microorganisms, also known as microbes, play important roles in many bodily functions. Bacteria, fungi, parasites, and viruses make up the microbiome, though bacteria have been the subject of most studies. Scientists estimate that 38 trillion microbes live in the human body, most of them in the gut microbiome.

Research shows that there may be more than 3,000 species of bacteria in the human gut microbiome.

 The gut microbiome plays an important role in digestion and keeping the immune system healthy.

 It consists of both beneficial and potentially harmful microbes. Both types of microbes can coexist peacefully, but various factors can upset that balance, including infections, dietary changes, and antibiotic use. Such disturbances in the microbiome may make you more susceptible to certain diseases.

You might see people using the words “microbiome” and “microbiota,” but they mean slightly different things. The microbiota refers to the microorganisms themselves, while the microbiome is the whole ecosystem, including the bacteria, their DNA, and their environmental conditions.

Symptoms and Conditions Associated With an Unhealthy Gut

Research suggests that the following signs throughout the body may be associated with an unhealthy gut microbiome. An imbalance of gut bacteria is known as dysbiosis.

Gastrointestinal Discomfort Frequent upset stomach characterized by gas, bloating, abdominal pain, diarrhea, and constipation can be a sign of irritable bowel syndrome (IBS). According to a review, imbalances in the gut microbiome may contribute to IBS in some people.

Fatigue Gut dysbiosis may impact the ability to process thoughts clearly in people with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), according to some researchers.

 ME/CFS is a condition characterized by at least six months of profound fatigue that rest does not relieve, along with symptoms that get worse after physical or mental effort.

 Notably, other reviews have stated that no evidence directly suggests that dysbiosis causes CFS, and the studies don’t often define patient populations well, mixing CFS in with other conditions like IBS. More research is needed to confirm the link.

Weight Gain Some evidence supports an association between obesity and disturbances in the gut microbiome. Dysbiosis may mean that you absorb more calories from food, and it may also sabotage your fat digestion, trigger constant low-level inflammation, and leave you feeling hungry, all of which can contribute to obesity. A review suggests that manipulating the gut microbiome may be a strategy to facilitate weight loss and prevent obesity in humans.

Autoimmune Diseases Research has examined whether gut dysbiosis may trigger or worsen certain autoimmune diseases, such as type 1 diabetes, multiple sclerosis, rheumatoid arthritis, and lupus. That said, more studies are needed to fully explore this potential link.

 Many studies exploring this link use rodent models, meaning it’s not necessarily accurate to apply their findings to humans. Also, people with these conditions often take medications like corticosteroids or biologics that can disrupt the gut microbiome, and studies can’t really differentiate between drug-induced and disease-induced dysbiosis.
Skin Conditions Imbalances in the gut microbiome have been linked to several skin disorders, including acne, atopic dermatitis, alopecia areata, and psoriasis. A balanced gut helps calm your immune system, keep inflammation in check, and process nutrients. If the microbiome is imbalanced, it can affect inflammatory or immune-mediated skin disorders.

Allergies An unhealthy gut microbiome, especially in early childhood, may play a role in allergies, including food and skin allergies. Researchers suggest that gut dysbiosis may weaken the gut lining, meaning proteins can leak into the bloodstream. After this leakage, an imbalanced gut may fail to signal to the immune system that these proteins don’t need to trigger an immune response, as occurs in people with allergies.

 More research is needed to fully understand the relationship between gut bacteria and allergies.
Mood Disorders There is a link between gut health and the brain through the gut-brain axis, and disturbances in the gut microbiome and inflammation in the central nervous system may contribute to mood disorders like depression and anxiety.

Migraine While more research is necessary to fully understand the connection, the gut-brain axis may also play a contributing role in migraine. The link might relate to a poorly functioning gut barrier, immune system activity, and brain inflammation.

How to Maintain or Rebuild a Healthy Gut

If you are worried that you may have an imbalance in your gut microbiome, talk to your doctor. A healthcare professional can help determine the potential cause of your symptoms and put together a treatment plan to help you feel better.

Several strategies can rebuild a healthy gut microbiome.

Increase your dietary fiber. Diet plays an important role in maintaining a healthy gut. If there’s an imbalance in the gut microbiome, one way to improve your gut’s balance is to increase your intake of dietary fiber. Only microbes living in the colon can break down and ferment dietary fiber, and this fermentation process releases short-chain fatty acids (SCFAs).

 According to research, SCFAs may help prevent the growth of the harmful bacteria Clostridium difficile (C. difficile), which can cause life-threatening diarrhea.

Foods that promote increased levels of SCFAs (sometimes referred to as prebiotics) include raw forms of the following:

  • Garlic
  • Onions
  • Leeks
  • Dandelion greens
  • Jerusalem artichokes
Bananas, seaweed, and asparagus are also good sources of prebiotics and fiber.

It’s important to introduce prebiotic foods slowly into your diet, as doing so suddenly can lead to increased gas and bloating. People with IBS may have difficulty digesting certain prebiotics, such as stone fruits.

Consume more probiotic food. Probiotics contain live organisms, usually specific strains of bacteria that can directly add healthy microbes to your gut.

 Foods containing probiotics include the following:

  • Yogurt
  • Kefir
  • Tempeh
  • Kombucha
  • Kimchi
  • Miso
  • Sauerkraut
You can also take probiotics in supplement form. However, the U.S. Food and Drug Administration (FDA) has not approved any health claims for probiotics.

 Labeling rules require only the total weight of microorganisms, which includes both live and dead cells, so the label may not reflect how many live, active bacteria are in the product when you take it.

 Talking with a healthcare professional before trying a probiotic supplement can help you decide whether one is a good fit. A healthcare provider can help you determine which probiotic supplement to try and point you to reputable brands. You can also explore reputable aftermarket supplement testing companies such as U.S. Pharmacopeia and ConsumerLab.com to find quality brands and products.
Maintain an exercise routine. Moderate physical activity — including strength training and cardio — can improve the diversity of healthy gut bacteria, the amount of SCFAs they produce, and their efficiency at using nutrients, according to a review. However, overdoing high-intensity exercise may increase gut leakiness and the resulting inflammation throughout the body, which can interfere with microbial balance.

Talk to your doctor about medications that can affect the gut microbiome. Certain medications can negatively impact gut health. Antibiotics are among the most significant disruptors to the balance of the gut microbiome. According to a review, antibiotic use can have several negative effects, including reduced species diversity, altered metabolic activity, and the growth of antibiotic-resistant organisms. Recovery of the microbiome can take months or even years, depending on the antibiotic and the person.

Research has found that several commonly used medications can alter the gut microbiome — some in positive ways and others in negative ways.

For example, one study examined the relationship between the gut microbiome and blood pressure medications, including beta-blockers, calcium channel blockers, diuretics, and angiotensin-converting enzyme inhibitors. Based on the researchers’ findings, these medications may affect the balance of the microbiota, and the microbiota may affect how your body metabolizes these medications and how well they work.

If you have any questions about how the medication you take might affect your gut microbiome, talk to your doctor.

Fecal Transplants Fecal matter transplantation (FMT) involves transferring the stool microbes of a healthy person into another person’s gastrointestinal tract to treat gastrointestinal issues.

 Healthcare professionals most often use this procedure to treat recurrent and severe infection of C. difficile colitis, the body’s response to a bacterial infection associated with diarrhea, abdominal cramping, and fever.

 The infection is often the result of antibiotic therapy, leading to an overgrowth of the harmful bacteria C. difficile in the gut that doesn’t respond to antibiotics and other measures.

A healthcare professional would first prescribe narrow-spectrum antibiotics to target C. difficile, typically fidaxomicin or, as an alternative, vancomycin.

 The FDA has also approved two microbiota-based products, Rebyota and Vowst, to help prevent a C. difficile infection from recurring. Vowst is the first FMT product that you can take by mouth.

On the Horizon: Research on the Gut Microbiome

The gut microbiome remains a promising area of research. Researchers are exploring home testing kits and finding further uses for fecal matter transplants.

Home Tests A number of startup companies have begun selling at-home testing kits to consumers, claiming they map their microbiomes. Many companies also promise that taking their vitamins and probiotic products will help improve disease symptoms and improve weight loss by correcting your microbiome.

However, there is not enough research on the accuracy of these tests and on what the facilities can actually achieve with the information they collect. In one small study, researchers at the National Institute of Standards and Technology sent identical portions of a single stool sample to seven at-home testing companies, three kits each, and found that results varied significantly. One company graded the same material healthy on two kits and unhealthy on a third.

The tests can also be pricey, and many require ongoing subscriptions to “rebalance” your microbiome over time. Talk to your doctor if you have any questions about at-home testing.

Fecal Matter Transplants for IBD

One review suggests that fecal transplants may help treat certain types of inflammatory bowel disease (IBD), such as ulcerative colitis, but more research is needed. Data on its uses in Crohn’s disease, another type of IBD, is inconsistent and only seems to provide short-lived benefits. Long-term data on the safety of FMT is also scarce, as this is still an emerging field; FMT has been highlighted as a potential ulcerative colitis treatment, but it needs longer-term analysis.

For now, the American Gastroenterological Association doesn’t recommend fecal transplants for ulcerative colitis or Crohn's disease except as part of a clinical trial.

Different Microbiomes in the Body

The gut microbiome gets plenty of attention from researchers. But various communities of microbes live throughout the human body, each making up its own microbiome that may contribute to your overall health in different ways.

Skin Microbiome

The surface of the skin also hosts a diverse microbiome, which interacts with the body’s immune system and affects dermatological health. The skin is home to millions of bacteria, fungi, and viruses. Many of these microbes are friendly and work with the body to prevent pathogen invasion and infection, as well as to accelerate wound healing.

Sometimes, when disharmony develops between helpful and unhelpful bacteria on the skin, certain conditions like acne, rosacea, and atopic dermatitis, a form of eczema, can result.

Oral Microbiome

The mouth is home to more than 500 species of bacteria that live primarily there. The oral microbiome performs key physiological functions that can benefit or harm the rest of the body, depending on its state.

Reproductive Microbiome

There is less research exploring the reproductive microbiome than that of the gut, skin, and mouth, but there is evidence that a plethora of microbes live in both the male and female reproductive organs.

 In women, the reproductive microbiome can be very dynamic and often changes as a result of factors like age, menstruation, and pregnancy.

 Less is known about the male reproductive microbiome, but recent studies show that it can significantly affect reproductive function and fertility in both sexes.

An earlier version of this article misspelled the drug name Rebyota as “Reybota.” 
EDITORIAL SOURCES
Everyday Health follows strict sourcing guidelines to ensure the accuracy of its content, outlined in our editorial policy. We use only trustworthy sources, including peer-reviewed studies, board-certified medical experts, patients with lived experience, and information from top institutions.
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