Is Bacterial Dysbiosis the Root of Your Gut Issues?

Written by: Will Cole, IFMCP, DNM, DC


Published on: February 23, 2023


Reviewed by: Denise John, PhD

Is Bacterial Dysbiosis the Root of Your Gut Issues?

Will Cole, IFMCP, DNM, DC, is a functional medicine practitioner and New York Times–bestselling author. His new book—Gut Feelings: Healing the Shame-Fueled Relationship between What You Eat and How You Feel—is available for preorder now.

What if I told you that you are less human than you think—more like a sophisticated host for the microbiome? Your digestive system is home to upwards of 100 trillion beneficial microbes, which is 10 times more than your own human cells.

The bacteria, fungi, viruses, and parasites that make up your gut microbiome dictate and influence a lot of important bodily processes related to your digestion, hormones, immune function, and mental and emotional health. (There’s a reason why it’s called the second brain. As you were developing in the womb, your gut microbiome was formed from the same tissue as your brain. And studies show that 95 percent of serotonin and close to 50 percent of dopamine are found in the gut.)

A healthy microbiome allows for healthy physical, mental, and emotional well-being. But for many people, there’s one thing standing in the way: bacterial dysbiosis, an imbalance in gut bacteria. As a functional medicine practitioner, I’ve often seen this gut problem be both a trigger as well as a symptom of health problems. (It’s something I see so often, it’s inspired my latest book, Gut Feelings, and informed the gut-feelings quiz I’ve created.)

  1. Will Cole Gut Feelings
    Will Cole Gut Feelings Bookshop, $26.04

What Is Bacterial Dysbiosis?

Your microbiome is a delicate ecosystem of various microbial species that live in harmony, working together to keep you healthy and thriving. Unfortunately, factors like medication overuse (particularly antibiotics, which can wipe out populations of good bacteria as well as kill bad ones), stress, and poor-quality foods can disrupt this essential balance of bacteria. As a result, “bad” bugs can start to replicate and grow, crowding out beneficial bacteria and causing an imbalance in the gut bacteria. This imbalance is also known as bacterial dysbiosis.

Common Types of Bacterial Dysbiosis

Since there are thousands of different strains of bacteria, there are numerous ways your gut can become imbalanced with an overgrowth of harmful bacteria. However, there are a few types of bacterial imbalance that are much more common than others, so they’re considered conditions and are specifically named.


Small intestinal bacterial overgrowth (SIBO), an increasingly common condition, happens when bacteria in the large intestine overgrow into the small intestine. This occurs when a process called the migrating motor complex (MMC) goes awry. Normally, when you’re not eating (in between meals or during extended fasting periods), bacteria in the small intestine move down into the large intestine, where most bacteria live. When this process isn’t working as well as it should, bacteria that are meant to migrate down instead stay (and replicate) in the small intestine, where they don’t belong.

When this happens, it can lead to a wide variety of digestive problems, such as irritable bowel syndrome (IBS), bloating, and acid reflux. And mental health issues, like anxiety and brain fog, can occur, too.

Candida Overgrowth

Candida refers to the Candida albicans fungus, which is the most common yeast in the human gastrointestinal system. Ideally, candida occurs in small amounts in our entire digestive tract as part of an overall healthy mycobiome balance (the prefix “myco-” indicates fungal species; the mycobiome are the fungal species that are part of the microbiome).

Sometimes, however, things can get knocked out of balance—often when there is a decrease in beneficial bacteria, such as when someone is taking a course of antibiotics or is on a diet high in sugar. And this allows candida to grow out of control. This can also create an environment where other opportunistic bacteria, yeasts, and parasites can take over and wreak havoc on your physical and mental health.

Signs and Symptoms of Bacterial Dysbiosis

Your gut influences many areas of your health, so symptoms of bacterial dysbiosis aren’t limited to gut dysfunction. Some of the most common signs and symptoms I see associated with bacterial dysbiosis include:

Testing for Bacterial Dysbiosis

If you think bacterial dysbiosis might be a problem for you, lab work is the first step in both conventional and functional medicine to determine the presence of dysbiosis. In my telehealth functional medicine clinic, I run the following labs:

  • SIBO breath test: Most often used to look for SIBO, this test measures the presence and amount of hydrogen and methane gas produced by the wayward bacteria in the small intestine. To complete the test, you’ll drink a solution containing a sugar, such as lactulose (most commonly used in SIBO tests), glucose, or xylose. If the bacteria are present, they will feed off the sugar and release hydrogen or methane gas.

  • Comprehensive stool analysis: By analyzing a sample of your poop, the lab will be able to identify what bacteria, yeasts, and fungi are present and whether there is any overgrowth of unwanted microbe strains.

  • Organic acids test: Similar to the hydrogen breath test, this test looks for the production of certain acids from negative microbe strains to determine whether there are any imbalances.

Treating Bacterial Dysbiosis

Once bacterial dysbiosis is identified, antibiotics are typically the next course of action in conventional medicine to mitigate the symptoms and kill off any bacterial overgrowth. However, as we see in functional medicine, this can be a vicious cycle because antibiotics don’t just kill off overgrowth; they also kill off the good bacteria needed for your overall health.

Functional medicine aims to treat the root cause behind bacterial dysbiosis, starting with the food we eat on a daily basis. The nutrients we eat are what the bacteria in our gut feed on and what determine whether the beneficial bacteria in our gut struggle or flourish. Remember, these bacteria have a huge influence on our mental health because they communicate directly with our brain by producing neurotransmitters like dopamine and serotonin, which largely regulate our mood and emotions.

Enterocytes—the cells that line your intestinal tract—regenerate every two to three weeks, which means significant changes in gut bacteria can happen within three days of making dietary changes. Although everyone’s exact way of eating is going to look different, limiting three key foods—sugar, alcohol, and processed foods—has been shown to help overcome bacterial dysbiosis and, in turn, help improve your mood and mental health.

  1. Sugar is the perfect fuel for all types of bad bacteria, including yeast overgrowth such as candida.

  2. Alcohol is a super saboteur of the gut-feeling connection. For one, it leads to microbiome issues and exacerbation of leaky gut. Research suggests that it can increase intestinal permeability and cause inflammation in other organs, including the brain. Another study published in Scientific Reports showed that people who drank a few times a week had lower total brain volume in early middle age (people from 39 to 45 years old). This is associated with brain fog, poor memory, mood changes, and other neurological symptoms impacting the gut-brain connection.

  3. Processed and prepackaged foods, at least most of them, lack the essential nutrients that gut bacteria need to flourish—fiber, especially prebiotic fiber, which is the food your bacteria eat. You can think of fiber as a type of fertilizer for your good gut bacteria, the ones that help regulate the nervous system and produce neurotransmitters. This type of dietary fiber is digested more slowly by your body and acts as a source of food for your gut’s healthy bacteria so they can multiply.

    Highly processed foods, which are generally low in fiber and prebiotic fiber, are associated with bad gut microbes linked to negative health markers. For example, one study published in the International Journal of Environmental Research and Public Health showed that participants who consumed fewer than three sources of fruits and vegetables daily had 24 percent higher odds of a diagnosis of anxiety disorder.

From there, my approach in functional medicine usually involves implementing herbal antimicrobials (such as cat’s-claw, oregano, and pau d’arco), probiotics, postbiotics (like butyrate), and binders (such as activated charcoal and zeolite).

Addressing Your Emotional Health

In addition to all the tools to support gut health directly, it is extremely important to consider the “feelings” side of things—your emotional health significantly influences your gut health.

The gut and the brain are intricately connected largely by one facet of the nervous system called the enteric nervous system (ENS), which is a division of the peripheral nervous system that lives within the walls of the gastrointestinal tract. The ENS communicates directly with the central nervous system, sending messages back and forth throughout your day and even when you sleep. That means that every time you feel a pang of anxiety, shame, happiness, or excitement, your brain and gut are communicating and responding accordingly.

With my patients, my approach to bacterial dysbiosis is to simultaneously implement mind-body practices like breathwork and meditation to support the vagus nerve (the longest cranial nerve in the body, involved in the gut-brain rest-and-digest aspect of our autonomic nervous system). When it’s needed, I will also coordinate therapy like EMDR (eye movement desensitization and reprocessing), somatic practices, and other trauma work to support the gut-brain axis of the nervous system.

Related Reading

Is Low-Fermentation Eating the Answer to SIBO?

Recovering Gut Health after Antibiotics

Irritable Bowel Syndrome (IBS)

We hope you enjoy the book recommended here. Our goal is to suggest only things we love and think you might, as well. We also like transparency, so, full disclosure: We may collect a share of sales or other compensation if you purchase through the external links on this page.

This article is for informational purposes only, even if and regardless of whether it features the advice of physicians and medical practitioners. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment and should never be relied upon for specific medical advice. The views expressed in this article are the views of the expert and do not necessarily represent the views of goop.