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.

The microbiome is composed of bacteria, fungi, parasites, and viruses, though bacteria are the most studied. Scientists estimate that 100 trillion microbes live in the human body, the majority of them in our gut microbiome.

Research shows 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.

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

Both types of microbes can coexist peacefully, but various factors can upset that balance, including infections, changes in diet, and use of antibiotics. Such disturbances in the microbiome may make an individual more susceptible to disease.

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 research, an imbalance of bacteria may trigger or exacerbate certain autoimmune diseases, like Crohn’s disease, ulcerative colitis, rheumatoid arthritis, and lupus. That said, more studies are needed to fully explore this potential link.

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

Allergies An unhealthy gut microbiome may potentially play a role in allergies, including food allergies and skin 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, and disturbances in the gut microbiome and inflammation in the central nervous system may contribute to mood disorders like depression and anxiety.

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

How to Maintain or Rebuild a Healthy Gut

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, and this fermentation process releases short-chain fatty acids (SCFAs).

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

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, among others. 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 probiotic food. 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 negatively impact 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.

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

For example, one study from 2022 explored the relationship between the gut microbiome and blood pressure medications, such as beta-blockers, calcium channel blockers, diuretics, and angiotensin-converting enzyme (ACE) inhibitors. Based on its findings, it seems that these medications may affect the balance of microbiota, and the microbiota may affect how these medications are metabolized and their level of effectiveness.

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 infection of Clostridium difficile (C. difficile) colitis, a bacteria 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 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 — although this potential still remains hypothetical.

Different Microbiomes in the Body

Outside of the gut, there are various communities of microbes that live throughout the human body, each making up its own microbiome:

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 the 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.

Editorial Sources and Fact-Checking

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