What is the Gut Microbiome? And Why It's Important to Your Health

There are trillions of microorganisms living in your gut — more cells than from your body itself! This collection of microorganisms, or microbes for short, make up what’s called the gut microbiome.

The human gut microbiome works with your body to help you break down food, process vitamins, and fight off foreign invaders (scientifically known as pathogens) to keep you healthy. It even communicates with your brain!

It's important to take care of your gut health and microbiome because it plays a major role in your body. 

What is The Gut Microbiome?

The gut microbiome is a complex community of microorganisms, most of which are bacteria, that live in the gut. These microorganisms consist of not just bacteria, but also viruses, fungi, and yeasts. It’s estimated that you have as many as 10 to 100 trillion microbes in your body.

A large portion of the gut microbiome is found in what’s called the “cecum”, which is essentially a pocket in the large intestine. Likewise, a large portion of the microorganisms in the microbiome are bacteria. It may come as a surprise, but there are actually slightly more bacterial cells in your body than your own cells. (1)

It’s estimated that the human microbiome weighs up to five pounds. (2)

It’s estimated that up to a thousand bacterial species are found in the human gut. (3) (4)

The microbiome essentially acts as an extra organ in the body and has a major impact on your health.

The Role of Probiotics in the Gut Microbiome

Image of probiotics spelled out in white pills on a blue surface

Research has shown that poor microbiome composition or an imbalance of microorganisms in the gut (also known as dysbiosis), is associated with disease. (5) The microbiota and the body communicate with each other and dysbiosis can lead to disrupted communications between microorganisms and their host (i.e. us), which can make us more susceptible to disease. (6)

One of the important things that probiotics do is they help break down food throughout the digestion process. They take dietary nutrients and convert them into metabolites, which play a role in the regulatory functions in the body. (5)

Probiotics improve the composition of the microbiome and can restore an imbalanced microbiota. Probiotics give beneficial functions to microbial communities in the gut, which may help prevent or decrease gut inflammation. (5) This is important because chronic inflammation, in the gut or otherwise, can be very harmful and is the root cause of many conditions. Gut inflammation, or inflammatory bowel disease, can result in symptoms such as persistent diarrhea, fatigue, abdominal pain, bloody stools/rectal bleeding, and more. (7)

Another way that probiotics help keep the microbiome in a healthy state is that they produce antimicrobial agents and metabolic compounds that suppress the growth of harmful microbes. (5) Probiotics, such as lactobacillus strains, strengthen the intestinal barrier, which may improve immune function. (8)

Quite a few studies have found that probiotics likely reduce the chances of experiencing diarrhea (from various causes) and duration of diarrhea is reduced. (9) (10) Some say that probiotics do this by repopulating the good parts of the microbiome and bringing it back into a good balance. 

The Role of Prebiotics in the Gut Microbiome

Image of 'prebiotic' spelled out in brown pills on a pink surface

Prebiotics are naturally-occurring plant fibers that your body can’t digest.

Prebiotics act as a food, or fuel source for probiotics. As a result, they encourage the growth of beneficial probiotics, which leads to a healthier microbiome and can reverse or improve a state of dysbiosis (the term for an unhealthy imbalance of the microbiome).

Nutrients for the intestines and digestive system are produced as a byproduct of this relationship between probiotics and prebiotics. (11) Some of these include nutrients such as acetate, butyrate, and propionate. (12) These are what are referred to as “short-chain fatty acids”.

Short-chain fatty acids are fatty acids that have less than six carbon atoms. They’re believed to play an important role in colon health and your overall health. It’s estimated that short-chain fatty acids may even account for about 10% of your caloric intake. (13)

Short-chain fatty acids play an important role in metabolizing carbohydrates and fats. (14)

Short-chain fatty acids are anti-inflammatories, which helps control inflammation in the gut. (15) (16) (17) This is worth noting because chronic inflammation has a host of unwanted side effects and is even at the root of certain conditions and diseases.

Some other benefits of short-chain fatty acids that you may have not known about include:

  • Reduction in diarrhea (18) (19)
  • May benefit people with IBS (20) (21) (22) (23)
  • Short-chain fatty acids appear to help regulate blood sugar levels, which is beneficial for people with diabetes in particular (24) (25)
  • In some animal studies, short-chain fatty acids were linked to weight loss and a reduction in fat storage. (26) (27) However, more research is needed in humans.
  • Some studies indicate that short-chain fatty acids reduce cholesterol, which is good for heart health and could lower the risk of heart disease. (28)

In addition to these health benefits as a result of being a food source for probiotics and producing short-chain fatty acids, prebiotics also facilitate healthy digestion by helping form healthy stools.

How Your Diet Affects the Gut Microbiome

Image of two women preparing a healthy meal

Eating a healthy diet is an important part of having a well-balanced microbiome. When you think about a healthy diet in general, what comes to mind is usually lean meats, lots of fruits and vegetables, and cutting back on unhealthy things like sugar, artificial sweeteners, and alcohol. You can follow similar guidelines for improving your gut health.

Fruits and vegetables should be front and center in a diet that’s good for the microbiome. They provide nutrients that the microbiome needs and they’re high in fiber. Your body can’t digest fiber, but good microbes in the microbiome do, which stimulate their growth.

Fermented foods are good for the microbiome because they contain probiotic strains, like bifidobacterium and lactobacillus. These probiotics make the microbiome more balanced towards good microbiota and crowd out bad, pathogenic microbes that cause illness. Some common fermented foods that are good for the microbiome include yogurt, sauerkraut, kimchi, tempeh, kefir, and kombucha.

Sugar and artificial sweeteners should be avoided if you want to have a healthy microbiome. Pathogenic microbes tend to feed on sugar and its substitutes, which has a number of side effects and can lead to infection.

The More Diverse Your Microbiome, The Better

Studies have shown that most healthy adults share more or less similar microbiome diversity. There is a correlation between less healthy individuals and lower microbiome diversity. For example, IBS patients have lower microbial diversity than healthy people. (29)

Microbiome diversity has a protective effect on human health. When you have lower microbiome diversity, you’re more susceptible to allergies and autoimmune diseases. (30)

Some have expressed concern about how microbiome diversity has gone down in people of Western cultures, likely due to diet. There is a fear that lower microbiome diversity could lead to permanent loss of certain probiotic species that are beneficial to human health. (31)

You can improve the diversity of your microbiome by eating a healthy, diverse diet, with an emphasis on plant-based foods. (32)

Why the Gut Microbiome is so Important to Your Health

The gut microbiome is made of trillions of microbes, both good and bad. You want that balance to be skewed towards the good microbes because otherwise, the harmful microbes, also known as pathogens, can cause infection and wreak all sorts of havoc on your body.

Colonization of the gut largely begins at birth and the amount and diversity of microbes that an infant is exposed to can have an impact on their health moving forward. (33) The gut microbiome plays an important role in the health and maintenance of the gastrointestinal tract from when you’re a baby and throughout your life. (34) (35)

There is a symbiotic relationship between the microbiome and their host. The microbiome influences risk of infection/disease, psychological/cognitive function, and overall health. The microbiome also improves digestion, produces and breaks down nutrients that the body can absorb, improves immune function, and more. (36)

Part of the reason that probiotics and the microbiome have an influence on your health is due to the gut-brain axis. The gut-brain axis is a fascinating communication system between the brain and the microbiome. Your brain and the microbes in your gut literally send signals back and forth to each other!

Your gut has 500 million neurons, which are cells that tell your body what it needs to know to function properly. (37) These neurons basically talk back and forth to the 100 billion neurons on your brain. The vagus nerve also plays a big role in the communication between the gut and the brain, sending signals in both directions. (38) (39)

Your brain and gut also communicate through neurotransmitters, which are chemicals that control emotions and feelings. Serotonin is probably the most widely known neurotransmitter, which controls feelings of happiness and regulates your bodily clock. (40) A large amount of serotonin is produced in the gut.

The microbes in your gut also produce a neurotransmitter called GABA (gamma-aminobutyric acid), which helps control feelings of anxiety and fear. (41) Studies in mice have shown that probiotics produce GABA in the gut, which reduces depression-related behaviors. (42)

Another reason why the microbiome is so important to your health is that it plays an important role in the immune system and regulating inflammation. (43)

Probiotics also play a major role in the gut-brain axis. Studies have shown that certain probiotic strains may relieve symptoms of anxiety, depression, and stress. (44) (45)

How The Gut Microbiome Affects Gut Health

The health of the microbiome is an important factor in gut health. If you have dysbiosis (an imbalance in the microbiome), you may experience symptoms such as abdominal pain, bloating, cramps, and more.

The gut microbiome also aids in digestion by helping you break down food and turning it into nutrients that the gut and body needs.

The composition of the gut microbiome has an effect on the development of the immune system and boosts the immune system by strengthening the intestinal barrier. (46) This makes it more difficult for you to be infected by pathogens in the gut.

The Gut Microbiome May Influence Your Weight

Image of a woman measuring her waist in front of a counter with healthy food

The two may seem unrelated, but the gut microbiome actually plays a role in your weight. However, researchers are basically just starting to scratch the surface of this topic. (47)

It’s not entirely clear how the gut microbiome has a positive influence on your weight but some researchers hypothesize that it’s through nutrient metabolism, regulating energy expenditure, and short-chain fatty acids. (47)

Some studies indicate that having a diverse microbiome has a preventative effect on weight gain. (48) Some studies have also shown a correlation with obesity and a less diverse microbiome. (49) There’s still much to be learned about this topic but considering the association between a more diverse microbiome and lower weight, it seems like a good idea to keep your gut microbes as diverse as possible!

The Gut Microbiome Helps Control Blood Sugar

Managing your blood sugar at a normal level is important for your health, particularly for your organs such as your eyes, heart, kidneys, and nerves. Researchers from a 2019 study concluded that “it is now well-established that imbalanced gut microbiota is linked to host glycemic control impairment and T2DM development”. (50) This means that if there’s an imbalance in your microbiome, you may be more likely to have unhealthy blood sugar levels and even be more susceptible to developing type 2 diabetes.

The Gut Microbiome and Mental Health

Image of a senior woman listening to relaxing music and doing yoga in a park

There’s a reason why we get “gut feelings”, a flash of clarity or intuition that can sometimes be uncomfortable or a fight or flight response that seems to come from our gut. These feelings don’t actually come from your gut, but the gut-brain axis makes it so that sometimes we register strong emotions as gastrointestinal distress, or that feeling of butterflies in your stomach.

This is just the tip of the iceberg when it comes to the connection between the gut microbiome, mental health, and the gut-brain axis.

Increasing evidence has shown correlations between the state of the gut microbiome and mental health. If your microbiome has a healthy balance, with more good microbes than bad, you’re more likely to be mentally well. If, on the other hand, you have dysbiosis (an unbalanced microbiome) and/or inflammation of the gut, your mental health is likely to be worse off. (51)

If you have dysbiosis of the gut, probiotics can restore your microbiome to a normal, healthy balance, so they have a potential role in improving anxiety, depression, and overall mental health. (51)

Not enough is known about probiotics to prescribe them as therapy for anxiety and depression, but recent research has shown that fermented foods have gastrointestinal and cognitive benefits. (52) (53) Also, there have been studies that specifically showed that “probiotics effectively mitigated anxiety and depressive symptoms similar to conventional prescription medications”. (51) It’s too soon to come to conclusions but these are exciting developments!

The Gut Microbiome and Cancer

Once we understand the complex relationship between the gut microbiome, immune system, and diet, it should clarify whether taking care of the microbiome can be a part of cancer prevention and treatment. (54)

Considering the growing number of studies done on probiotics and the microbiome, researchers from Cancer Cell said that “it is becoming increasingly clear that modulation of the gut microbiota may represent a novel and important adjunct to current anti-cancer therapeutic modalities”. (55) In other words, probiotics on their own aren’t going to cure cancer, but it’s possible that they may be considered an effective supplement along with traditional cancer treatment.

More studies are needed to understand the underlying molecular interactions between the microbiota and cancer. (55)

The Gut Microbiome and Autism

Autism spectrum disorder results in a number of difficulties with language and social interactions. Researchers want to know whether there is a connection between the gut microbiome and autism.

Studies show that kids with autism spectrum disorder have a mixture of gut microbes that are noticeably different from kids without ASD. Research now suggests that gut microbes not only play a role in digestion but they also influence brain function and social development. (56)

While some of the results of the studies on the connection between the microbiome and autism look promising, it’s still early and researchers emphasize that larger trials with control groups are necessary. (56)

The Takeaway

The gut microbiome is made up of trillions of microbes that coexist with each other and human cells.

While some bacteria and other microbes can harm and infect us, others are harmless or benefit human health. Harmful microbes that cause infection are called pathogens. Beneficial microbes are referred to as probiotics.

The gut microbiome plays a role in digestion, metabolism, immune health, brain health, and more.

Your gut microbiome develops early in life and is influenced by how you were delivered as a baby and your genetics. Later in life, it can be influenced by your diet, age, stress levels, environment, illness, and use of medication.

The health of your microbiome can be reduced by things like poor diet, inflammation, and getting sick. You can improve the health of your microbiome by eating a healthy diet rich in probiotics and prebiotics. You can also conveniently improve your gut health by taking probiotic supplements and prebiotic supplements.


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