Digestive Health

What Is the Gut Microbiome?

The microbiome consists of trillions of bacteria, fungi, parasites, and other microbes that play a vital role in the body’s day-to-day functions.

Ashley Welch
By Medically Reviewed by 
Reviewed:
Medically Reviewed

While it may not be the most pleasant thing to think about, our bodies harbor communities of bacteria and other microorganisms both inside and on our skin. These microorganisms, also known as microbes, play an important role in many of the body’s functions.

In addition to bacteria, fungi, parasites, and viruses also make up the microbiome, although bacteria is the most studied. Scientists estimate that 100 trillion microbes live in the human body, the majority of them in our gut.

The microbiome is made up of both beneficial and potentially harmful microbes.

The majority are friendly and have a symbiotic relationship with the body, meaning both the microorganism and the body benefit. Some microbes, however, are pathogenic, meaning they can lead to disease and illness. In a healthy person, both types of microbes coexist and interact with each other peacefully. But various factors can upset that balance, including infections, change in diet, and long-term use of antibiotics. Such disturbances in the microbiome may make an individual more susceptible to disease.

Different Microbiomes in the Body

Various communities of microbes live throughout the human body, each making up its own microbiome:

Gut Microbiome Most microbes in the body are located in the gut. The largest numbers are found in the small and large intestines. The gut microbiome is the most talked about and most studied microbiome in the body. Studies show that there may be more than 1,000 species of bacteria in the human gut microbiome.

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

Disturbances to the gut microbiome can contribute to diseases, such as obesity, inflammatory bowel disease, diabetes, eczema, celiac disease, and psoriatic arthritis.
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 and accelerate wound healing.

Sometimes when there is disharmony between friendly and unfriendly bacteria on the skin, certain conditions like acne and atopic dermatitis, a form of eczema, can result.
Oral Microbiome The mouth hosts the second largest microbiome after the gut, with more than 700 species of bacteria.

The microbiome in the mouth plays an important role in digestion, as well as oral health and overall health of the body.
Reproductive Microbiome There has not been as much research on the reproductive microbiome as 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 scientists believe that this microbiome can have significant effects on reproductive function and performance in both sexes.

Symptoms of an Unhealthy Gut

Research suggests that signs of an unhealthy gut can be seen throughout the body:

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

Fatigue Chronic fatigue syndrome, a condition characterized by extreme fatigue that lasts for at least six months, may be linked to an imbalance in the gut microbiome, according to researchers, who also found that nearly half of people with chronic fatigue syndrome also had IBS.

Weight Gain There is evidence of an association between obesity and disturbances in the gut microbiome. A study suggests that manipulating the gut microbiome may be a strategy to facilitate weight loss and prevent obesity in humans.

Autoimmune Diseases According to a study, a specific kind of bacteria found in the gut called Bacteroides fragilis produces a protein that may trigger the onset of certain autoimmune diseases, like ulcerative colitis, rheumatoid arthritis, and multiple sclerosis.

Skin Conditions Imbalances in the gut microbiome can contribute to several skin disorders, including acne, atopic dermatitis, or eczema, and psoriasis.

Allergies An unhealthy gut microbiome can play a role in allergies, including food allergies and skin allergies.

Mood Disorders There is a link between gut health and the brain, and disturbances in the gut microbiome and inflammation in the central nervous system may contribute to mood disorders like depression and anxiety.

Migraines While the connection isn’t fully understood, the gut-brain connection may also play a contributing role in migraines.

How to Maintain or Rebuild a Healthy Gut Microbiome

If you are worried 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 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 return to gut homeostasis is to increase your intake of dietary fiber.

Dietary fiber can only be broken down and fermented by microbes living in the colon. This fermentation process releases short-chain fatty acids (SCFAs), which lower the pH of the colon. The lower pH creates an environment that prohibits the growth of some harmful bacteria, such as Clostridium difficile.

Foods that promote increased levels of SCFAs (sometimes called prebiotics) are raw forms of garlic, onions, leeks, asparagus, bananas, seaweed, dandelion greens, and Jerusalem artichokes. It’s important to introduce prebiotic foods slowly into your diet, as doing so suddenly can lead to an increase in gas and bloating.

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

Foods containing probiotics include yogurt, kefir, tempeh, kombucha, kimchi, miso, and sauerkraut.
Probiotics can also be taken in supplement form. However, like all supplements, these are not fully regulated by the Food and Drug Administration, like medications are. This means that probiotic pills may not contain the amount of probiotic advertised on the label, or even that the bacteria is alive and active at the time you take it. It’s best to talk to your doctor before trying any probiotic supplement.

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 to find quality brands and products.
Maintain an exercise routine. Physical activity can improve the health of gut bacteria. A small study found that an exercise program of just six weeks had a positive impact on participants’ gut microbiomes.

Talk to your doctor about medications that can affect the gut microbiome. Certain medications can have a negative impact on gut health. One of the biggest disruptors to the balance of the gut microbiome is antibiotics. According to a review, antibiotic use can have several negative effects on the gut microbiome, including reduced diversity of species, altered metabolic activity, and the growth of antibiotic-resistant organisms.

Additional research found that several commonly used medications can alter the gut microbiome — some in positive ways and some in negative ways.

Proton pump inhibitors, which are medications that treat acid reflux, have been linked to negative effects on the gut microbiome. On the other hand, medications to treat high blood pressure and high cholesterol, including diuretics, beta blockers, and statins, have been linked to a healthier composition and function of gut bacteria.

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

On the Horizon: Research on the Gut Microbiome

The gut microbiome remains a promising area of research, with many avenues:

Home Tests A number of startup companies have begun selling at-home testing kits to consumers with the claim that they map out their microbiome. Many companies also promise that vitamins and probiotics will help improve disease symptoms and improve weight loss by correcting your microbiome. However, not enough research exists on the accuracy of these tests and what can be done with the information they detect. Talk to your doctor if you have any questions about at-home testing.

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

The procedure is most commonly used to treat recurrent and severe C. difficile colitis, a condition associated with diarrhea, abdominal cramping, and fever. The condition is often the result of antibiotic therapy, leading to an overgrowth of the harmful bacteria C. difficile in the gut that is not responsive to antibiotics and other measures.
One research review suggests that fecal transplants can be helpful in treating inflammatory bowel disease, but more research is needed.

The same review also suggests that fecal transplantation may be used in the distant future to treat other chronic conditions in the future, such as obesity, chronic fatigue syndrome, fibromyalgia, metabolic syndrome, and multiple sclerosis.

Editorial Sources and Fact-Checking

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