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The bacteria and other microbes in your gut help you digest food and may support immune, heart, and brain health, among other benefits.

Your body is full of trillions of bacteria, viruses and fungi. They are collectively known as the microbiome.

While some bacteria are associated with disease, others are actually extremely important for your immune system, heart, weight and many other aspects of health.

This article serves as a guide to the gut microbiome and explains why it’s so important for your health.

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What Is the Gut Microbiome?

Bacteria, viruses, fungi and other microscopic living things are referred to as microorganisms, or microbes, for short.

Trillions of these microbes exist mainly inside your intestines and on your skin.

Most of the microbes in your intestines are found in a “pocket” of your large intestine called the cecum, and they are referred to as the gut microbiome.

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

In fact, there are more bacterial cells in your body than human cells. There are roughly 40 trillion bacterial cells in your body and only 30 trillion human cells. That means you are more bacteria than human (1, 2).

What’s more, there are up to 1,000 species of bacteria in the human gut microbiome, and each of them plays a different role in your body. Most of them are extremely important for your health, while others may cause disease (3).

Altogether, these microbes may weigh as much as 2–5 pounds (1–2 kg), which is roughly the weight of your brain. Together, they function as an extra organ in your body and play a huge role in your health.

The gut microbiome refers to all of the microbes in your intestines, which act as another organ that’s crucial for your health.

How Does It Affect Your Body?

Humans have evolved to live with microbes for millions of years.

During this time, microbes have learned to play very important roles in the human body. In fact, without the gut microbiome, it would be very difficult to survive.

The gut microbiome begins to affect your body the moment you are born.

You are first exposed to microbes when you pass through your mother’s birth canal. However, new evidence suggests that babies may come in contact with some microbes while inside the womb (4, 5, 6).

As you grow, your gut microbiome begins to diversify, meaning it starts to contain many different types of microbial species. Higher microbiome diversity is considered good for your health (7).

Interestingly, the food you eat affects the diversity of your gut bacteria.

As your microbiome grows, it affects your body in a number of ways, including:

• Digesting breast milk: Some of the bacteria that first begin to grow inside babies’ intestines are called Bifidobacteria. They digest the healthy sugars in breast milk that are important for growth (8, 9, 10).
• Digesting 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 (11, 12, 13, 14, 15, 16, 17).
• Helping control your immune system: The gut microbiome also controls how your immune system works. By communicating with immune cells, the gut microbiome can control how your body responds to infection (18, 19).
• Helping control brain health: New research suggests that the gut microbiome may also affect the central nervous system, which controls brain function (20).

Therefore, there are a number of different ways in which the gut microbiome can affect key bodily functions and influence your health.

The gut microbiome affects the body from birth and throughout life by controlling the digestion of food, immune system, central nervous system and other bodily processes.

The Gut Microbiome May Affect Your Weight

There are thousands of different types of bacteria in your intestines, most of which benefit your health.

However, having too many unhealthy microbes can lead to disease.

An imbalance of healthy and unhealthy microbes is sometimes called gut dysbiosis, and it may contribute to weight gain (21).

Several well-known studies have shown that the gut microbiome differed completely between identical twins, one of whom had obesity and one of whom did not. This demonstrated that differences in the microbiome were not genetic (22, 23).

Interestingly, in one study, when the microbiome from the twin with obesity was transferred to mice, they gained more weight those that had received the microbiome of the other twin, despite both groups eating the same diet (22).

These studies show that microbiome dysbiosis may play a role in weight gain.

Fortunately, probiotics are good for a healthy microbiome and can help with weight loss. Nevertheless, studies suggest that the effects of probiotics on weight loss are probably quite small, with people losing less than 2.2 pounds (1 kg) (24).

Gut dysbiosis may lead to weight gain, but probiotics can potentially restore gut health and help reduce weight.

It Affects 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) (25, 26, 27).

The bloating, cramps and abdominal pain that people with IBS experience may be due to gut dysbiosis. This is because the microbes produce a lot of gas and other chemicals, which contribute to the symptoms of intestinal discomfort (28).

However, certain healthy bacteria in the microbiome can also improve gut health.

Certain Bifidobacteria and Lactobacilli, which are found in probiotics and yogurt, can help seal gaps between intestinal cells and prevent leaky gut syndrome.

These species can also prevent disease-causing bacteria from sticking to the intestinal wall (29, 30).

In fact, taking certain probiotics that contain Bifidobacteria and Lactobacilli can reduce symptoms of IBS (31).

A healthy gut microbiome controls gut health by communicating with the intestinal cells, digesting certain foods and preventing disease-causing bacteria from sticking to the intestinal walls.

The Gut Microbiome May Benefit Heart Health

Interestingly, the gut microbiome may even affect heart health (32).

A recent study in 1,500 people found that the gut microbiome played an important role in promoting “good” HDL cholesterol and triglycerides (33).

Certain unhealthy species in the gut microbiome may also contribute to heart disease by producing trimethylamine N-oxide (TMAO).

TMAO is a chemical that contributes to blocked arteries, which may lead to heart attacks or stroke.

Certain bacteria within the microbiome convert choline and L-carnitine, both of which are nutrients found in red meat and other animal-based food sources, to TMAO, potentially increasing risk factors for heart disease (34, 35, 36).

However, other bacteria within the gut microbiome, particularly Lactobacilli, may help reduce cholesterol when taken as a probiotic (37).

Certain bacteria within the gut microbiome can produce chemicals that may block arteries and lead to heart disease. However, probiotics may help lower cholesterol and the risk of heart disease.

It May Help Control Blood Sugar and Lower the Risk of Diabetes

The gut microbiome also may help control blood sugar, which could affect the risk of type 1 and 2 diabetes.

One recent study examined 33 infants who had a genetically high risk of developing type 1 diabetes.

It found that the diversity of the microbiome dropped suddenly before the onset of type 1 diabetes. It also found that levels of a number of unhealthy bacterial species increased just before the onset of type 1 diabetes (38).

Another study found that even when people ate the exact same foods, their blood sugar could vary greatly. This may be due to the types of bacteria in their guts (39).

The gut microbiome plays a role in controlling blood sugar and may also affect the onset of type 1 diabetes in children.

It May Affect Brain Health

The gut microbiome may even benefit brain health in a number of ways.

First, certain species of bacteria can help produce chemicals in the brain called neurotransmitters. For example, serotonin is an antidepressant neurotransmitter that’s mostly made in the gut (40, 41).

Second, the gut is physically connected to the brain through millions of nerves.

Therefore, the gut microbiome may also affect brain health by helping control the messages that are sent to the brain through these nerves (42, 43).

A number of studies have shown that people with various psychological disorders have different species of bacteria in their guts, compared to healthy people. This suggests that the gut microbiome may affect brain health (44, 45).

However, it’s unclear if this is simply due to different dietary and lifestyle habits.

A small number of studies have also shown that certain probiotics can improve symptoms of depression and other mental health disorders (46, 47).

The gut microbiome may affect brain health by producing brain chemicals and communicating with nerves that connect to the brain.

How Can You Improve Your Gut Microbiome?

There are many ways to improve your gut microbiome, including:

• Eat a diverse range of foods: This can lead to a diverse microbiome, which is an indicator of good gut health. In particular, legumes, beans and fruit contain lots of fiber and can promote the growth of healthy Bifidobacteria (48, 49, 50, 51).
• Eat fermented foods: Fermented foods such as yogurt, sauerkraut and kefir all contain healthy bacteria, mainly Lactobacilli, and can reduce the amount of disease-causing species in the gut (52).
• Limit your intake of artificial sweeteners: Some evidence has shown that artificial sweeteners like aspartame increase blood sugar by stimulating the growth of unhealthy bacteria like Enterobacteriaceae in the gut microbiome (53).
• Eat prebiotic foods: Prebiotics are a type of fiber that stimulates the growth of healthy bacteria. Prebiotic-rich foods include artichokes, bananas, asparagus, oats and apples (54).
• Breastfeed for at least six months: Breastfeeding is very important for the development of the gut microbiome. Children who are breastfed for at least six months have more beneficial Bifidobacteria than those who are bottle-fed (55).
• Eat whole grains: Whole grains contain lots of fiber and beneficial carbs like beta-glucan, which are digested by gut bacteria to benefit weight, cancer risk, diabetes and other disorders (56, 57).
• Try a plant-based diet: Vegetarian diets may help reduce levels of disease-causing bacteria such as E. coli, as well as inflammation and cholesterol (58, 59).
• Eat foods rich in polyphenols: Polyphenols are plant compounds found in red wine, green tea, dark chocolate, olive oil and whole grains. They are broken down by the microbiome to stimulate healthy bacterial growth (60, 61).
• Take a probiotic supplement: Probiotics are live bacteria that can help restore the gut to a healthy state after dysbiosis. They do this by “reseeding” it with healthy microbes (62).
• Take antibiotics only when necessary: Antibiotics kill many bad and good bacteria in the gut microbiome, possibly contributing to weight gain and antibiotic resistance. Thus, only take antibiotics when medically necessary (63).

Eating a wide variety of high-fiber and fermented foods supports a healthy microbiome. Taking probiotics and limiting antibiotics can also be beneficial.

The Bottom Line

Your gut microbiome is made up of trillions of bacteria, fungi and other microbes.

The gut microbiome plays a very important role in your health by helping control digestion and benefiting your immune system and 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.

To help support the growth of healthy microbes in your gut, eat a wide variety of fruits, vegetables, whole grains and fermented foods.