What is the Gut Microbiome and Why Is Everyone Talking About It?

Fact Checked by Dr. Rachel Adams, PhD, RDN
A colorful representation of the gut microbiome

In this article, we’ll cover the following topics all about the gut microbiome:

  1. What is the Gut Microbiome? A Quick Overview
  2. What Does the Gut Microbiome Do for Our Health?
  3. The Gut Microbiome Impact: The Broad Range of Linked Health Conditions and Diseases 
  4. What Lives in the Gut Microbiome: Good Guys and Bad Guys
  5. Improving the Gut Microbiome for Specific Healthful Results
  6. Your Gut Microbiome — The Key to Unlocking Vibrant Health

What is the Gut Microbiome? A Quick Overview

Inside your intestinal tract live about 100 trillion bacteria that form a symbiotic community that’s responsible for the regulation of many of our bodily functions. (1, 2)

Experts now believe it should be considered an organ, just like your heart or lungs. (3)

And that’s exactly how critical this community of microorganisms is to your health. (4, 5)

Without it, our immune systems couldn’t function properly, and neither could our brains. (6, 7) It’s an extremely complex and completely crucial part of how our bodies function.

So, why is everyone starting to discuss this ‘microbiome’ now — the mysterious organ that we didn’t learn about in school?

Because the gut microbiome plays a key role in our overall health AND we have the power to influence it. 

Unlike most of our organs, the microbiome isn’t a static, unchanging entity. It’s constantly being altered and re-populated by what we eat. (1, 8)

An image of the bacteria originating from the large intestine

In the same way we can use exercise to improve our physical fitness and heart health, or lift weights to build our muscles, we can take specific actions to optimize our gut microbiome. (9, 10)

When you consider the sheer number of bacteria (aka microbiota) in your gut (in the average person there are over 4 pounds of microscopic organisms and more than 1000 different species in there!), it brings a whole new meaning to the adage, “You are what you eat.” (2)

What Does the Gut Microbiome Do for Our Health?

Breakthroughs in science and technology are uncovering the many ways that the gut microbiome influences overall health. Based on these advancements we now know a lot more about how your gut is the control center for your health (and we are learning more about this amazingly complex ecosystem inside of us every day).

an image showing intestinal flora affecting health conditions
Image credit: drjockers.com

Some of the critical bodily functions these bacteria are responsible for include:

  • Immune system regulation (11, 12)
  • Food digestion (13)
  • Blood sugar regulation (14, 15)
  • Vitamin production (2)
  • Brain chemical influence (7, 16)
  • Heart health management (17)

Basically, there’s not much that goes on in your body that doesn’t involve the gut microbiome in some way. 

If you are dealing with a nagging health issue, odds are it may be connected to your gut.

The Gut Microbiome Impact: The Broad Range of Linked Health Conditions and Diseases 

Because of all the ways the gut microbiome impacts bodily functions, it’s understandable that a balanced and healthy microbiome = a healthier person. (5)

And unsurprisingly, research concludes that many diseases that plague modern society correlate to the health of the gut microbiome. 


Diabetes and pre-diabetes have been directly tied to gut microbiome health. Significant compositional differences in gut microbiota were observed between the diabetic group and the non-diabetic group. (18)  Furthermore, clinical studies found that type 2 diabetic individuals who were not receiving medicinal intervention had fewer short-chain fatty acid (short chain fatty acids are the products of bacterial fermentation in the gut. More on this later…) producers in their gut microbiome as compared with a healthy population. (19

Although the research regarding the relationship between microbiome and metabolic syndromes is still emerging, more and more evidence and data suggest that microbiome dysbiosis plays an essential role. (20)

Amazing, right? It is really hard to imagine that the tiny bugs inside of the gut are that important in metabolism homeostasis. It might be too early to talk about intervention of diabetes via gut microbiome, but based on current clinical evidence, increasing butyrate (one of the short-chain fatty acids we discussed earlier) producing bacteria and supplementing Lactobacillus and Escherichia species with metformin could be a potential approach to managing blood sugar more effectively.  (19)

This gives massive amounts of hope to those battling diabetes or pre-diabetes because it means effective blood sugar regulation may be influenced by a balanced gut microbiome.    

Heart Disease

Your heart health is also influenced by the strength of your microbiome. Scientific discovery is observing relationships between the health of the gut and cardiovascular health. In studies, researchers have found a correlation between gut health and the development of atherosclerosis, hypertension and heart failure. (17, 21)

Keeping the gut strong can lead to an increase in healthy cholesterol levels and a decrease in chemicals known to cause artery blockage. 

In some studies, probiotic supplementation has also been shown to positively impact lipid profiles. (22, 23)  Probiotics are live cultures of bacteria, which, when properly selected and delivered in adequate amounts, can increase the presence of healthy bacterial colonies in our guts.

As you can see, the way certain bacteria behave and metabolize foods can impact the way your heart functions. 

Certain bacteria in your gut can promote high-density lipoprotein (HDL) — the good cholesterol. (21)

For these reasons, we have to focus on making our gut health a top priority for better heart health. 

Intestinal Diseases

It’s probably no surprise that the gut microbiome significantly affects overall digestive health since it is located at the center of your digestive system. In fact, the gut microbiome plays a crucial role in maintaining proper digestive health by helping improve bowel regularity and decreasing symptoms of gas, bloating, diarrhea and leaky gut. (13, 25, 26)

However, beyond those basic digestive functions, research is also uncovering a direct parallel between certain gut bacteria species and chronic diseases like irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), Crohn’s disease, ulcerative colitis, celiac disease, and even colorectal cancer. (27, 28, 29, 30, 31)

You see, when the bacteria in the gut process certain types of undesirable food, they produce gases and byproducts that can be toxic to the intestinal tract at worst, and uncomfortable at best. (25)

Luckily, as with heart disease, reviews of the available data indicate that if probiotic and prebiotic supplementation is done correctly, it can play a role in supporting healthy management of intestinal disorders. (32) This involves identifying the correct beneficial species and nutrient sources that will create positive bacterial changes in the gut. 

Again, it’s great news for all of us who are striving for good digestive health, as it appears the stronger the good bacteria in our microbiome, the better our digestive system functions. 

Proper digestive health also influences leaky gut, a condition that affects millions of people worldwide. When our gut microbiome is in tip-top shape, it helps ensure that our immune system functions properly so we don’t get sick as often. (6, 12) When it’s functioning at its best, it creates a strong intestinal wall, which prevents harmful bacteria from entering the bloodstream and improves symptoms of leaky gut.


In many ways, the health of your microbiome can have a direct impact on your weight.  That’s right, studies show that a having high-functioning and diverse colony of bacteria in your gut means you’re less likely to be obese. (33)

A healthy gut means your metabolism can function at its best. After all, our gut is the place where we digest food, so it can affect absorption of nutrients and storage of fat. And, when certain species of health-promoting bacteria decline within the microbiome, metabolic health declines as well. (14)

Furthermore, this phenomenon has even been observed in twins. (34) When one twin was obese and one was thin, changes in the makeup of their microbiomes could be observed. This means that even when two organisms have practically the same genetic makeup, they can have completely different microbiomes — giving researchers hope that targeting and modulating the microbiome (either therapeutically or through strategic nutritional intervention) can reduce the incidence of obesity.

The gut microbiome also synthesizes certain vitamins, which can impact weight gain/loss. Vitamin K and certain B vitamins are produced by the microbiome colony. (59)

Mental Health

In what has been dubbed the “gut-brain connection,” scientists have discovered in more detail the mind-blowing ways the microbiome directly influences our levels of anxiety, depression, and even our overall mood. (7, 35, 36)

This may not come as a surprise to anyone who’s ever experienced gastrointestinal upset because they were nervous about something. This is an acute example of how the gut and brain are linked.

In fact, up to 95% of serotonin (the happy hormone) can actually be found in the gut, not the brain. (37) So in many ways, our happiness is directly connected to the levels of a healthy digestive system and the associated bacteria we have in our gut. 

And while science is still trying to figure out exactly how to treat these mental health conditions specifically through altering the microbiome, one thing is clear: people with depression are missing certain species of bacteria from their gut. (38)

What Lives in the Gut Microbiome: Good Guys and Bad Guys

Most of the bacteria that comprise the microbiome are there for your protection and benefit. These “good guys” form a type of army that provides defense and protection for your entire body. (39)

Imagine having an army of a trillion microscopic organisms overwhelming and destroying most anything that tries to compromise your health…this is exactly the way a properly functioning and balanced gut microbiome works.

But when things in the gut become unbalanced, the other, more sinister “bad guys” can start causing problems.

There are plenty of strains of what we may consider pathogenic bacteria, viruses, or fungi that have their place in very small numbers in a normal gut microbiome. The problem is, when the good guys aren’t flourishing, a void can be created that the bad guys quickly fill…and they’re able to wreak havoc on your health. (40)

When the good guys aren’t strong enough to keep opportunistic bad guys in check, they produce toxins that wear down the lining of the colon, allowing these bad guys to escape and infect the bloodstream or tissue. (39, 41) This is where you get sick. Really sick. They can also cause inflammation in your body and can even lead to chronic diseases.  

And this is why we want to make sure we do whatever we can to promote the health of the good bacteria — they will simply take care of the bad ones for us, allowing us to stay in control of our health and minimize the chances of getting chronic diseases. 

Improving the Gut Microbiome for Specific Healthful Results

an illustration of prebiotics and probiotics

So, how exactly do we most effectively encourage the good guys and eradicate the bad guys within the gut?

There are a few key ways to accomplish this task.

1. Prebiotics

Prebiotics are the most potent tool we have at our disposal in the fight against bad gut bugs in the colon.

Prebiotics are superfoods that feed the beneficial bacteria in your gut and make them strong. (42)

There are few different types of prebiotics, most of which are categorized by the FDA as dietary fibers as they mostly pass through your digestive system without breaking down or being digested and have beneficial properties on your health. A super-powered class of prebiotic fiber is called resistant starch, which is a unique type of carbohydrate which bypasses digestion in the small intestine and is slowly fermented in the large intestine. (43) Resistant starch is the preferred food of the beneficial bacteria in the colon. (44, 45)  When resistant starch is consumed, a very important byproduct is produced called short-chain fatty acids (SCFAs) — butyrate being one important example. (46) SCFAs have been identified as the primary mechanism through which the microbiome promotes healing throughout the body, including providing additional benefits on overall colonic health, leaky gut, and much more. (47, 48, 49, 50)

Furthermore, these resistant starches help control blood sugar levels, help you manage blood lipids, and offer the benefits of fiber without increasing your “net carb” consumption. (51, 52, 53)

Basically, they’re the key to keeping a proper balance in your gut microbiome and ultimately, your entire body.

2. Probiotics

Also known as beneficial bacteria, incorporating probiotics into your gut-health regime can be another effective way to improve the diversity and health of your gut microbiome. There are multiple studied strains of probiotic bacteria that have been researched to promote the health of your gut. (54) Unfortunately, the reality is that not all probiotics are as reliable as we’ve been told to think they are. (55, 56)

In fact, probiotics found in some supplements and food products fail to even reach the gut in large enough numbers to colonize and produce beneficial effects in the body. (55)  This is true for a few reasons. First, some probiotics strains have difficulty surviving the harsh, acidic digestive tract. So, these kinds of probiotic strains don’t actually make it all the way to your gut in order to make a difference in your gut health. 

Secondly, while there are many researched strains of beneficial probiotics, everyone’s microbiome is unique. Only a few commercially available probiotic strains that are well-studied and are the ones that you specifically need, are the same ones that are being used in store-bought probiotics. And lastly, even if enough of the probiotic bacteria survive the digestive process and make it to the gut, it’s likely those beneficial strains of bacteria might eventually die off. This is because probiotics need to consume abundant amounts of prebiotic fiber to effectively grow (in strength and numbers) and colonize — and almost none of us get enough fiber in our diets!   

3. Rest

One of the most important things we can do for our health is to prioritize sleep. And, as it turns out, our gut microbes like it when we rest too.

Recent studies are linking the health and diversity of the microbiome to the quality of sleep and vice versa. (57, 58)

It’s another important reason to try to squeeze in those crucial 7-9 hours of sleep each night. 

4. Reduce Stress

Reducing stress is another one of those things we know we need to do for better health, but here’s another reason we need to consider stress management…you guessed it, the gut microbiome is negatively affected by stress. (59)  Emerging research on the gut-brain axis indicates that the connections between your gut and your brain are strong and bi-directional (7) — In other words maintaining a healthy gut microbiome can improve mental health, and reducing stress levels can support a healthier microbiome. Additional research is required to fully understand the connection between the two and how to effectively manipulate it.

In order to improve your microbiome health, you should evaluate places in your life that you can effectively reduce stress (of course that is sometimes easier said than done). You may want to consider meditation or other self-care rituals that help you maintain a healthy sense of balance in your life — both have been shown to lower stress levels.

Your Gut Microbiome — The Key to Unlocking Vibrant Health

The gut microbiome, the organ you didn’t even know you had, is truly one of the most impactful areas of the body to target when looking for ways to improve health. 

By supporting our good bacteria in our guts, we’re supporting our entire body. 

From weight control to blood sugar regulation and mental health, the healthier our guts are, the healthier we are. 


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