Friday, March 17, we will be closed and will re-open and resume shipping on Monday, March 20.

FREE Domestic shipping for orders $150+

Detox Learning Center

The Microbiota-Gut-Brain Axis: How Your Gut and Brain Are Connected

The microbes and nerves in your body work together like musicians in an orchestra. They play a big role in the health of your mind and body.

You might think your brain is controlling what “music” is played, but it’s not that simple. The community of microbes in your gut — your microbiota — greatly influences what happens in your body. 

Your gut microbiota sends “notes” to your brain. These impact your brain function, gut health, and more. If bad players are on board, health issues can arise. That includes problems like anxiety, depression, poor memory, and leaky gut. (1, 2

Fortunately, there are many things you can do to help ensure your microbiota-gut-brain axis plays in harmony. That includes things like reducing your toxin load and clearing infections.

Ahead, find out how the microbiota-gut-brain axis works. Learn what disrupts it and ways to help restore balance in your “orchestra.” 

What Is the Microbiota-Gut-Brain Axis?

What Is the Microbiota-Gut-Brain Axis?

Scientists have known for a long time that your gut and brain “talk” to each other. A newer discovery is that there’s a third party in this conversation: your gut microbiota. This trio makes up your microbiota-gut-brain axis. (3)

Your gut contains a diverse group of microorganisms. These are predominantly bacteria but also include fungi and other pathogens. A community of microbes is a microbiota. The collection of genes housed by these microbes is a microbiome. That said, some people use the term microbiome to refer to whats technically the microbiota. (4, 5)

You start to “collect” these microbes either during birth or while you’re still in your mother’s womb. Newer research suggests it’s the latter. After you’re born, you accumulate microbes from your diet and the environment. (6, 7, 8)

Your microbiota makes up a more significant portion of your body than you may realize. You have about one microbe for every one of your human cells. The vast majority of bacteria are in your colon. But they’re also on or in your skin, eyes, and other areas of your body. (2, 3, 9)

You and your gut microbiota can live in a mutually beneficial relationship. You provide room and board for bacteria. While nestled in your colon, they munch on fiber and other remnants of digestion. In turn, they can support the health of your mind and body. (10, 11)

Your gut microbiota interacts with your brain and enteric (gut) nervous system. Here’s a closer look at how the gut-brain connection works.

Your second brain

The enteric nervous system is like a “second brain,” but it’s in your gut rather than in your head. So, it’s sometimes called your gut-brain.

Have you ever had stomach cramps or discomfort? It’s your gut-brain that enabled you to feel these unpleasant sensations. 

Within the walls of your digestive tract are 100–500 million neurons (nerve cells). These make up your enteric nervous system. That’s the largest group of neurons in your body. This network of nerves extends from your esophagus to your anus. It makes more than 30 different neurotransmitters (nerve messengers). (12)

Your gut microbiota influenced the development of your enteric nervous system when you were a baby. A well-functioning enteric nervous system is important. It helps control many functions of your small and large intestines. (13)

More specifically, your enteric nervous system regulates: (12)

  • Blood flow to your intestines
  • Gut secretion of fluids, electrolytes, and hormones
  • Movement of your intestinal contents
  • Intestinal barrier function, allowing nutrient absorption
  • Immune activity in your gut

Your enteric nervous system can do all this without direct input from your brain. It usually does communicate with your brain, but it doesnt need to for many functions. (14

Another ongoing source of input for your gut-brain is your microbiota. 

Your microbiota is like a little factory inside your gut. It makes neurotransmitters, such as serotonin and dopamine. They enable communication between your gut and brain. (15, 16, 17)

The microbes in your gut also make short-chain fatty acids. Examples are propionate and butyrate. Certain bacteria produce these when they munch on dietary fiber in your gut. These fatty acids participate in the communication between your gut and brain. For example, they help control inflammation. (18)

To understand how these microbial products convey messages, it helps to know a little about the communication routes between your gut and nervous system.

Communication routes

Scientists have identified a few different “routes” that messages from your gut can take to “talk” with your nervous system. (19)

For example, when microbes release neurotransmitters, some “stay local.” They convey messages within the enteric nervous system in your gut. Others travel via your bloodstream to your brain. (2)

Another important communication route is via your vagus nerve. It begins in the base of your neck and extends into your abdomen. It connects with your intestines and other organs. (19)

Technically, you have two vagus nerves — there's one on each side of your body. They’re like a two-way street. They carry messages from your gut to your brain and vice versa. (12)

But the number of “lanes” on each side of the street aren’t equal. There’s about one nerve fiber going down to your gut for every eight going up to your brain. That means there is a lot more traffic” or messages traveling from your gut to your brain than in the other direction. (12)

So, your brain gets a lot of feedback from your gut. But your brain also sends some messages to your digestive tract. 

For example, the brain-to-gut messages sent via your vagus nerve control the release of stomach acid and digestive enzymes. They also help regulate inflammation levels, appetite, and your body’s response to stress. (12)

The messages your vagus nerve carries are heavily influenced by your microbiota. When microbes release neurotransmitters and short-chain fatty acids, these can activate your vagus nerve. (2, 15)

When your microbiota is diverse and includes more “good” microbes, you’ll have better “messaging.” But when your gut bacteria are out of balance, the communication changes. You’re more likely to develop mental health issues, brain dysfunction, and gut problems. (2

Risks of an Unhealthy Microbiota-Gut-Brain Axis

Risks of an Unhealthy Microbiota-Gut-Brain Axis

An imbalance in your microbiota is like a poorly organized orchestra that has too many drums and not enough violins. You may have too many harmful bacteria and not enough helpful ones. So, the good guys are overpowered. 

This imbalance in your gut microbiota is called dysbiosis. Inflammation and oxidative stress can significantly increase when you have dysbiosis. As a result, chronic illness becomes the new soundtrack to your life. (20

Here’s a look at some of the health problems that may result when your gut-brain connection is disrupted.

Anxiety, depression, and other mental health challenges

Experts used to view mental health “from the top down.” They believed that symptoms of anxiety, depression, and other mental health challenges were due to an imbalance in your brain. But that idea is evolving with new research. 

Scientists now think that gut dysbiosis could be one of the root causes of imbalances in your brain. In other words, your gut health could be intricately linked to your mental health. (21)

For example, when your microbiota is out of balance, it makes less butyrate. This short-chain fatty acid helps calm inflammation. If you have less butyrate on board, inflammation could increase. When the nerves in your brain are inflamed, you’re at a higher risk of depression. (18)

Less butyrate may also result in increased intestinal permeability. That’s also known as leaky gut. This “leakiness may lead to increased inflammation and a higher risk of mental health challenges. (22, 23)

For example, gut dysbiosis is common in people with autism. In one observational study, 43% of kids with autism had increased intestinal permeability. But kids free of autism didnt have leaky gut. (24)

Disruption of your microbiota-gut-brain axis is also linked with insomnia. And poor sleep increases your risk of emotional challenges, including anxiety and depression. (25)

Animal research suggests that restoring specific microbes in your gut microbiota may help combat anxiety and depression. But more research is needed. (25)

Poor brain function

Gut dysbiosis may impair your memory and other brain functions. It may increase your risk of Alzheimer’s disease and other types of dementia. Gut dysbiosis is also associated with cognitive problems in Parkinson’s disease. (26)

Certain gut microbes are linked with better memory and brain function, according to animal studies. But an excess of other gut microbes is linked with brain inflammation, oxidative stress, and brain plaque. (26)

Have you ever misplaced your keys or walked into a room and forgotten why you went there? Maybe it’s time to consider the role of gut dysbiosis in your memory lapses.

Some research suggests that bad gut microbes cause disordered proteins to clump in your brain, forming plaque. That could prevent your brain cells from working right. This is like a rogue musician linking arms with the other musicians so they can’t play their instruments. (27

This protein clumping may contribute to Parkinson’s disease and Alzheimer’s disease. As more clumping occurs, the symptoms of the disorders worsen. The music stops playing, so to speak. (26, 27)

Gut disorders

You already know that your gut houses a large portion of the microbes in your body. So, it shouldn’t be surprising that disrupting your microbiota-gut-brain axis can lead to digestive tract issues.

Researchers have linked gut dysbiosis with several digestive tract problems, including: (28, 29)

  • Gastroesophageal reflux disease (GERD)   
  • Gastritis
  • Diarrhea
  • Constipation
  • Irritable bowel syndrome (IBS)
  • Crohn’s disease
  • Ulcerative colitis
  • Celiac disease
  • Colorectal health issues
  • Stomach health issues

For instance, people with IBS and diarrhea tend to have less “good” bacteria. That includes Bifidobacteria and Lactobacilli. And these people have more Enterobacter bacteria, which can lead to disease when your defenses are down. (28, 30, 31)

Someday, scientists may be able to pinpoint which microbes could calm various chronic gut conditions. But more research is needed. (29)

Other issues

When something in your gut-brain connection goes awry, problems don’t always stay in the axis. And issues in the rest of your body can also affect the axis.

Studies suggest that your gut microbiota can affect your:

  • Immune system: Upsetting your gut microbiota balance could be a factor in autoimmune diseases. Some of these include type 1 diabetes, rheumatoid arthritis, lupus, vitiligo, psoriasis, eczema, and multiple sclerosis. (32)
  • Liver function: The makeup of your gut microbiota is vastly different in liver disease. For example, people with non-alcoholic fatty liver disease tend to have fewer bacteria that make butyrate. As mentioned earlier, a drop in butyrate is linked with depression. (28, 33)
    • Heart health: Human and animal studies suggest gut dysbiosis may promote heart disease. That includes atherosclerosis (narrowing of your arteries), high blood pressure, and heart failure. (11
    • Breathing: The severity of asthma has been linked to harmful microbes dominating your gut. The bad bacteria may promote inflammation in your airways. (34)
    • Weight: Growing evidence suggests gut microbes can affect your weight. The gut microbiota of lean people is quite different from obese people. (1, 35) 

    In some cases, such as obesity, researchers aren’t sure which comes first. Does gut dysbiosis lead to the disease or vice versa? Future research will help clarify these connections.

    What Disrupts Your Microbiota-Gut-Brain Axis?

    What Disrupts Your Microbiota-Gut-Brain Axis?

    Many factors can wreak havoc with your microbiota-gut-brain axis. You can’t control all of them. But you do have control over many things that can disturb this crucial connection.

    Keep reading for some of the key culprits that disrupt your microbiota, gut, and brain.

    Heavy metals

    Toxic heavy metals can throw a wrench into cellular processes and damage your mitochondria. Some heavy metals are in air pollutants, water, and amalgam dental fillings among many other sources. Avoid them when you can. Gut microbes may provide some defense.

    Animal research suggests your microbiota may help protect you against toxic heavy metals. When mice without a microbiota were exposed to heavy metals, they absorbed more cadmium and lead. (36)

    But other animal research suggests that exposure to heavy metals may decrease some beneficial gut microbes. Unfortunately, many of these are bacteria that produce butyrate. As mentioned earlier, butyrate may help protect against leaky gut and depression. (37

    Glyphosate and other pesticides

    Glyphosate — commonly sold under the name Roundup — is a pesticide widely used to control weeds in crops. Some pesticides are also used to kill insects. 

    One way some of these chemicals harm “pests” is by disrupting the mitochondria of the bugs or plants. But there are some other “bugs” — the good microbes in your gut — that may be harmed by these chemicals. (38)  

    Lab studies suggest glyphosate may kill off good microbes in your gut. But some bad bugs like Clostridium and Salmonella are resistant to the chemical. So, the bad bacteria may start to overpopulate your gut if you don't have enough good bugs to keep them in check. (39)

    When bad bacteria like Clostridium overgrow, they produce high levels of harmful compounds that are toxic to your brain. That may contribute to emotional issues and neurological disorders, such as Parkinson’s disease. (39

    Also, animal studies suggest the pesticide chlorpyrifos may upset the balance of microbes in your gut. This pesticide is used on some corn, soybeans, fruit trees, nut trees, and cruciferous vegetables like broccoli. (40, 41, 42)

    Animal research also suggests chlorpyrifos could promote obesity. This may be due to its ability to shift the composition of your gut microbiota. (40)


    Contrary to popular belief, parasitic infections are not rare. They’re very common. And parasites can disrupt your microbiota-gut-brain axis. These parasites include single-celled protozoans and helminths (worms). (43, 44)

    Animal and human studies suggest that protozoan and helminth parasites can evoke long-lasting changes in your gut microbiota. This may contribute to issues such as intestinal inflammation and leaky gut. (45, 46, 47)

    One study found that children infected with Giardia and Ascaris parasites had an unfavorable shift in their gut microbiota. Some scientists suspect that parasitic disruption of kids’ gut microbiota may harm their brain function and behavior. More research in this area is needed. (43, 47)


    Dangerous pathogens can interact with your genes, including those involved in inflammatory bowel diseases. Animal research suggests that some pathogens promote the expression of genes related to Crohn’s disease and ulcerative colitis. Those are the two main types of inflammatory bowel disease. (48, 49)

    Inflammatory bowel diseases are marked by increased intestinal permeability or leaky gut. If your gut barrier isn’t working well, that gives harmful pathogens a route to your brain. (50)

    Also, the inflammatory products of dangerous pathogens may contribute to brain disorders like Alzheimer’s disease. This could be especially true as you get older. Your blood-brain barrier weakens with age. So, inflammatory compounds have easier access to your brain. (51)

    Scientists have found certain pathogens in regions of the brain affected by dementia or memory loss. For example, herpes has been linked with Alzheimer’s disease. (3)

    Low-fiber, high-sugar diet

    Helpful bacteria munch on fiber in your colon. But what happens if you don’t give them the fiber they need? The microbes don’t get fed. 

    If you don’t “feed” your good gut bacteria, they can’t make protective short-chain fatty acids like butyrate. As a result, you’re more vulnerable to dysbiosis and leaky gut. And over the long term, good bacteria won’t stick around if you don’t feed them. (5, 52)

    A high-sugar diet can also lead to dysbiosis and leaky gut. When rodents were fed a sugary diet, they had unhealthy shifts in their microbiota. And they had a 2.5-fold increase in gut permeability. (53)

    But don’t reach for artificial sweeteners instead. Animal studies suggest that sucralose, aspartame, and saccharin could promote gut dysbiosis. The artificial sweeteners may also increase gut inflammation. (5)

    Antibiotics and other drugs

    Antibiotics are prescribed to kill microbes that cause infections. But the drugs can wipe out much of your helpful bacteria. That enables harmful microbes — including Candida albicans and Clostridium difficile — to quickly multiply. (54)

    As you take more antibiotics, harmful microbes can get stronger. They may become resistant to the drugs. Meanwhile, your good microbes get weaker. That further increases the microbial imbalance in your gut. And that disrupts your microbiota-gut-brain axis.

    But antibiotics aren’t the only type of drug that harms your microbiota and gut-brain. Other medications that can disrupt your microbiota include: (55, 56, 57)

    • Non-steroidal anti-inflammatory drugs (NSAIDs)
    • Proton pump inhibitors for acid reflux 
    • Metformin, a medication for type 2 diabetes
    • Some psychiatric drugs, such as for bipolar disease

    In a lab study, scientists exposed 40 different good gut bacterial strains to more than 800 non-antibiotic drugs. About 24% of the medicines prevented at least one species of gut bacteria from growing. (55)


    Food and the environment are laced with trace amounts of chemicals, such as from plastics and flame retardants. They accumulate in the food chain. And some harmful chemicals are generated when you cook meat. Your gut microbiota is exposed to these toxins when you eat. (58)

    Your gut bacteria may break down some of these chemicals. For example, one lab study found that good gut microbes can transform harmful chemicals from grilled meat into less toxic compounds. (59)

    But your gut microbiota’s actions on toxic chemicals aren’t always in your favor.

    In some cases, bacteria produce more harmful toxins when they break down chemicals. That may trigger the release of inflammatory molecules, which could damage your gut wall. (58)

    Not only that, but the chemicals may trigger gut dysbiosis. When mice ate food that was tainted with bisphenol A (BPA) a chemical used in some plastic containers  their microbiota changed. It became similar to the imbalanced microbiota of mice fed a high-sugar diet. (60)  


    Stress may disrupt the composition and activity of your gut microbiota. Your gut microbes can recognize and respond to your hormones and neurotransmitters. That includes ones involved in your body’s stress response. (61)

    Both mental and physical stress can disrupt your microbiota. That includes stressors like fear, lack of sleep, test-taking, harsh physical training, extreme temperatures, and excess noise. (62

    When stress affects your gut microbes, it could promote dysbiosis, leaky gut, and inflammation. For example, scientists have found that stress can cause a drop in beneficial Lactobacillus. That bacteria helps protect the health of your gut wall. (62, 63, 64)

    Also, when you’re under stress, your gut-brain and vagus nerve signal your digestive tract to reduce its activity. Slower digestion reduces the availability of nutrients to your beneficial gut microbes. (62

    Restore Your Microbiota-Gut-Brain Axis

    Restore Your Microbiota-Gut-Brain Axis

    Clearly, many factors could disrupt your microbiota-gut-brain axis. So, how do you maintain or restore harmony in your gut-brain connection?  

    Simply put, remove toxins and pathogens inhibiting the growth of good microbes. And make diet and lifestyle choices that support a healthy microbiota.

    Clear out toxins

    Whether youre dealing with harmful heavy metals, glyphosate, or plastics, these toxins don’t belong in your body. Regularly binding and removing toxins is essential for a healthy microbiota.

    Consider taking herbs to support good elimination. During detox, make sure you’re pooping 2 or 3 times a day. You don't want toxins loitering in your colon.

    A big help in toxin removal are binders. They help clear out toxins like heavy metals and glyphosate. These nutrients bind toxins tightly so they can be carried all the way out of your body via your poop.

    Combat infections

    Don’t let pathogens and parasites wipe out entire sections of your microbial “orchestra.” That encourages the growth of microbes you don’t want. 

    Use dietary support with antipathogenic properties since this may help curb infections and strip out harmful pathogens embedded in the DNA of your cells. (65, 66, 67)  

    In addition, you can do a parasite cleanse to kick out freeloaders that disrupt your microbiota. Take parasite-killing herbs and help your body eliminate parasites.

    Clean up your diet

    What you regularly eat can have a significant impact on your microbiota. Processed foods low in fiber and nutrition inhibit the growth of the microbes you want. And they may support the growth of the bacteria you don’t want. (68)

    Ditch the sugar and other refined carbs that feed parasites. But don’t replace sugar with artificial sweeteners. Instead, satisfy your sweet tooth with whole fruits.

    Fruits, vegetables, and other plant-based foods supply prebiotics, which are “food” for your good bacteria. Some phytochemicals and fiber in plant foods are prebiotics. That’s one of the many reasons these foods are recommended in healthy diets. (69, 70)

    You can also enjoy fermented foods, such as fermented cabbage or other fermented vegetables. If you tolerate fermented dairy products like yogurt and kefir, those are also options. These generally contain live bacteria that may help replenish your microbiota. (68, 71)  

    Make healthy lifestyle choices

    A healthy lifestyle is important to support your microbiota. Here are a few ways you can protect your gut-brain connection:

    • Enjoy physical activity: Animal research suggests that exercise promotes the growth of bacteria that produce butyrate. This beneficial short-chain fatty acid supports gut health. Low-intensity activities like walking count, so do what you’re able. (72)
      • Control stress: You can’t avoid all stress, but you can manage it. Evaluate your schedule to see what you can eliminate. Seek out positive social interactions. 
      • Try meditation: Meditation may help to lower inflammation, decrease your body’s response to stressful situations, and reduce your risk of leaky gut. (73)   
      • Check medications: If you’re taking prescription medications, research whether they disrupt microbiota. And don’t take an antibiotic unless it’s essential to get better. (54)
      • Avoid smoking: Smoking may increase gut microbes that are associated with Crohn’s disease. Plus, smoking raises your risk of colorectal health issues (not to mention a host of other health problems). (74)

      Back in Harmony

      When your microbiota and gut-brain connection are in sync, you’re more likely to enjoy the rhythms of good health. It’s like a well-conducted orchestra.

      But toxins, infections, drugs, and poor lifestyle choices can alter your microbiota. As a result, your health may be more like clanging symbols — chronic illness. That could include mental health challenges, brain disorders, gut issues, and more.

      To help restore harmony to your microbiota-gut-brain axis, you need to clear out heavy metals, pesticides, and other toxins. Get help from binders and herbs that promote regular pooping. You can also take herbs to kill parasites

      Healthy food choices, stress management, and a little physical activity could also help restore harmony to your gut-brain connection.

      Is your microbiota-gut-brain axis out of sync? What steps will you take to tune it?