The bacteria and other microbes that live in your gut are known as your “gut microbiome.” They help you digest food and may support immune, heart, and brain health. However, disruption in your gut microbiome is linked with certain health conditions.

Microorganisms, or microbes, include bacteria, viruses, fungi, and other microscopic living things.

Trillions of these microbes exist inside your intestines and on your skin. It’s often said that microbial cells outnumber human cells in your body. However, some more recent research suggests the ratio is closer to roughly equal but varies among individuals.

Although many types of microbes live inside you, bacteria are the most studied.

While some bacteria are associated with disease, others are crucial for your immune system, heart, weight, and overall health.

What is the gut microbiome?

Most intestinal microbes are found in a “pocket” of your large intestine called the cecum.

There are up to 1,000 species of bacteria in the human gut microbiome, each playing a different role in your body. Most are essential for your health, while others may cause disease. The balance of types of bacteria is also important.

  • Your body is home to trillions of bacteria, viruses, and fungi, collectively known as the microbiome. Microbes that reside in your gut are part of your gut microbiome.

Where does your gut microbiome come from?

Humans have evolved to live with microbes over millions of years. During this time, microbes have developed important roles in the human body. In fact, without your gut microbiome, it would be very difficult to survive. Additionally, the microbes rely on us, their host, for survival, too.

The gut microbiome starts to develop the moment you are born. You are exposed to microbes when you pass through your mother’s birth canal. New evidence suggests that babies may even come into contact with some microbes inside the womb.

As you grow, your gut microbiome diversifies, meaning it starts to contain many different types of microbial species. Higher microbiome diversity is considered good for your health.

Many factors can shape your gut microbiome, including sleep, medications (such as antibiotics), environment, and the food you eat. Research has shown that within days of changing your diet, your gut microbiome can change, too.

The gut microbiome: Key roles

Digesting Nutrients: Certain bacteria digest complex carbohydrates and fibers, producing beneficial compounds called short-chain fatty acids. These support gut lining health and may protect against obesity, diabetes, and certain cancers.

Digests fiber: Certain bacteria digest fiber, producing short-chain fatty acids, which are important for gut health. Fiber may help prevent weight gain, diabetes, heart disease, and the risk of cancer.

Helps regulate your immune system: The gut microbiome also affects how your immune system works. By communicating with immune cells, it can manage how your body responds to infection.

Helps brain and nervous system: Research suggests that the gut microbiome may also affect the central nervous system, which controls brain function.

Protects the body: The gut microbiome helps defend against microbes and toxins that can cause harm.

Gut Barrier Protection: Friendly bacteria occupy space and resources, preventing harmful microbes from colonizing the intestinal wall.

How does your gut microbiome affect your weight?

An imbalance of healthy and unhealthy microbes is sometimes called gut dysbiosis, and it may contribute to weight gain.

Studies suggest the gut microbiome could affect how many calories your body extracts from the food you eat.

Studies in mice have shown that the gut microbiome can affect total body fat. Mice given the microbiome from obese mice extracted more calories from their food and had higher body fat than mice given microbiota from lean mice.

Some scientists think probiotics could be a useful addition to help weight management in people with obesity.

How does your gut microbiome affect your gut health?

The microbiome can also affect gut health and may play a role in intestinal diseases like irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD).

The bloating, cramps and abdominal pain that people with IBS experience may be due to changes in the gut microbiome. This is because the microbes produce a lot of gas and other chemicals, which contribute to the symptoms of intestinal discomfort.

However, certain healthy bacteria in the microbiome can also improve gut health. Lactobacilli, which are found in probiotics and yogurt, produce lactic acid, which helps with digestion.

These species can also prevent disease-causing bacteria from sticking to the intestinal wall. Taking certain probiotics that contain Bifidobacteria and Lactobacilli may help reduce symptoms of IBS, as they may be lacking in people with this condition. However, each person can react differently to probiotics and different strains can also have varying effects.

However, stress is also thought to affect the microbiota, which could lead to changes in the gut microbiome. Indeed, psychological stress is associated with conditions such as IBS. While stress could be a factor in IBS development, it’s not thought to cause IBD. However, stress may worsen symptoms.

How does your gut microbiome affect your heart?

The gut microbiome may affect heart health. A 2015 study of 1,500 people found that it plays an important role in promoting “good” HDL cholesterol and triglycerides.

Certain unhealthy species in the gut microbiome may contribute to heart disease by increasing levels of a chemical called TMAO, which can lead to blocked arteries and potentially result in heart attacks or strokes. These bacteria convert specific nutrients, such as choline and L-carnitine found in red meat and other animal-based foods, into TMAO, increasing the risk of heart disease.

However, other bacteria within the gut microbiome, particularly some strains of Lactobacilli, may help reduce cholesterol when taken as a probiotic.

Does your microbiome affect blood sugar and diabetes?

The gut microbiome is also thought to play a role in blood sugar and diabetes.

One 2015 study of 33 infants with a genetically high risk of developing type 1 diabetes found that the diversity of the microbiome dropped suddenly before the onset of the disease. Also, the number of unhealthy bacterial species increased just before the onset of the disease.

Another 2015 study showed that blood sugar levels could vary greatly even when people ate the same foods, likely due to the types of bacteria in their guts.

How does your gut microbiome affect your brain?

The gut microbiome may affect brain health in a number of ways. Certain species of bacteria can help produce chemicals called neurotransmitters. These chemicals transmit signals to and from your brain. Serotonin is a neurotransmitter that’s mostly made in the gut. In fact, 95% of your body’s serotonin is produced here. (However, this serotonin cannot enter the brain).

Additionally, your gut is connected to your brain through millions of nerves. Scientists think the gut microbiome may also be involved in brain health by affecting the messaging through these nerves, particularly the vagus nerve. The communication between the gut and the brain is known as the gut-brain axis.

A number of studies have shown that people with various neurological disorders have different species of bacteria in their guts compared with those without the disorder. This suggests that the gut microbiome may be playing a role in brain health.

Some studies have also shown that certain probiotics can improve symptoms of depression and other mental health disorders.

It’s unclear, though, whether the microbiome causes the brain symptoms or the other way round. A 2022 review suggests a bidirectional relationship, where psychological stress actually changes the gut microbiome itself.

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The Bottom Line

Your gut microbiome is made up of trillions of bacteria, fungi, and other microbes. It plays an important role in your health by helping to control digestion, benefiting your immune system, and promoting many other aspects of health.

An imbalance of unhealthy and healthy microbes in the intestines may contribute to weight gain, high blood sugar, high cholesterol, and other disorders.

You can help support the balance of healthy microbes in your gut by eating a wide variety of fruits, vegetables, whole grains, and fermented foods.