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What Is Gut Dysbiosis? 7 Signs To Watch For

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What Is Gut Dysbiosis? 7 Signs To Watch For

Gut health is an essential foundational piece of optimal well-being. When our microbiome is balanced and functioning well, we generally experience good health and optimal digestion.

Unfortunately, chronic gut issues, ranging from constipation to bloating and acid reflux symptoms, are increasingly common, affecting roughly 70 million Americans each year.

While these symptoms can be a sign of many different things, the root cause of digestive problems is often gut dysbiosis. If you truly want to get to the bottom of your nagging digestive symptoms, read on to learn everything you need to know about your microbiome, why dysbiosis is so common, and how to restore balance to your gut for optimal health.


What is Gut Dysbiosis?

Dysbiosis occurs when there is an imbalance of good vs. bad microorganisms in the gut. There is a risk of damaging and unwanted symptoms when there is an imbalance, ranging from brain fog and fatigue to constipation or other gastrointestinal symptoms.

Gut dysbiosis can refer to a few different scenarios:

  • A lack of diversity in the types of microbes you have in your gut
  • A deficiency of beneficial gut microbes, or
  • Having too much growth of harmful bacteria.  

An imbalanced microbiome can trigger pro-inflammatory cascades in the body and contribute to immune dysregulation associated with various conditions, such as autoimmune diseases.

Gut Dysbiosis Signs and Symptoms

There are many different signs and symptoms that can indicate a state of dysbiosis in the gut, and they can differ widely from person to person.

The most common gut-related symptoms include gas and bloating, constipation, acid reflux, diarrhea, bad breath, abdominal pain, and mucus in the stool.

For some individuals, symptoms can affect mental health, such as anxiety, trouble with focus or concentration, depression, chronic fatigue, or brain fog.  

Dysbiosis can also impact the skin, with signs and symptoms including acne, eczema, dark circles under the eyes, psoriasis, dandruff, and atopic dermatitis.

What Causes Gut Dysbiosis?

While there are many suspected causes of gut dysbiosis, it's likely that a combination of factors ultimately is at the root of the issue.  


A diet that is inflammatory, high in refined sugar, processed foods, and poor-quality fats, can result in dysbiosis by supporting the growth of pathogenic microbes over beneficial microbes and driving inflammatory processes in the gut and body in general. A lack of fiber has also been linked to a higher risk for dysbiosis.  


Pathogenic infections can be picked up through food and water sources, wreaking havoc on the gut microbiome and contributing to imbalances. If you've had a bad case of food poisoning, it's important to consider the longer-lasting impact of the infection on your microbiome!

Chronic Antibiotic Use

A history of antibiotic use or certain medications can also contribute to dysbiosis. Overuse of antibiotics has been linked in many studies to disruption of microbial balance in the gut.


Antacids and proton pump inhibitors, commonly prescribed for acid reflux, can reduce the stomach's acidity over time, which negatively impacts the natural barrier (an acidic environment) that prevents bacteria growth in the stomach and upper intestine.  

Lifestyle Factors

Lifestyle factors like chronically high-stress levels, poor sleep patterns, regular alcohol consumption, and smoking can all contribute to dysbiosis by adding stress to the body, creating inflammation, and reducing the efficacy of the immune response in general.

Both chronic and acute stress can shift the gut bacteria in the inside (lumen) and border (mucosal lining) of the gut.

Chronic stress can increase the permeability of the gut lining, resulting in a "leaky gut," allowing bacteria from the gut to escape into circulation, increasing inflammation in the body. Additionally, chronic stress can lead to a prolonged elevation of cortisol levels in the body, which negatively impacts the immune system by increasing mast cells and decreasing the production of lymphocytes. This can lead to an increased risk of infections and microbial imbalances.  

Dental Hygiene

Poor dental hygiene is another factor to consider when looking for the root cause of dysbiosis, particularly in the case of long-term gum inflammation, as seen in cases of periodontitis.

While in a healthy individual, stomach acid likely destroys bacteria traveling from the oral cavity through saliva, sometimes oral bacteria translocate to the gut causing immune dysregulation and microbiome imbalances.

Oral bacteria can also enter the bloodstream through the gums and travel throughout the body, increasing inflammation systemically.  

How Dysbiosis Affects Health

When you have Gut Dysbiosis, you may start to experience a variety of health conditions as a result. Dysbiosis can lead to inflammation and joint pain, skin issues, chronic fatigue, heartburn, anxiety, depression, and a myriad of other symptoms.

While these symptoms can be due to many different factors, having an imbalanced microbiome may mean that you could have a more challenging time recovering. Dysbiosis can contribute to many chronic health conditions over time, including:

  • Irritable Bowel Syndrome (IBS)
  • Candida overgrowth
  • Allergies
  • Colitis
  • Polycystic ovarian syndrome
  • Skin conditions, such as eczema
  • Obesit

Working with your doctor can help clarify the root cause of your health issues and determine if dysbiosis is a contributing factor.

How to Test for Dysbiosis

With the help of your practitioner, a combination of functional lab tests can help give insight into what's going on with your gut microbiome.  

Comprehensive Digestive Stool Analysis (CDSA)

A comprehensive stool test can evaluate the structure and function of the gut. This test looks at how efficiently you can digest and absorb food and inflammatory markers and potential pathogens such as candida species and various parasites. Many of these tests also offer zonulin as an add-on option (discussed in more detail below).

*Some CDSA tests also analyze a fecal sample for a comprehensive list of every microbe detected, so your practitioner can make more specific recommendations for what foods or supplements may help rebalance the gut.

*The GI-Effects comprehensive stool test is a unique option. It offers a microbial antibiotic susceptibility to determine which prescriptive, and natural antibiotics are most effective on each patient's microbiome, which is important for individualized treatment options.

Intestinal Permeability Screen

Dysbiosis is often associated with a "leaky gut," also known as increased intestinal permeability, a state in which there is a loss of regulation over molecules that pass in and out of the gut wall.

Testing for the biomarker zonulin also allows for assessing the integrity of the epithelial lining of the gut. Zonulin is a peptide that plays a role in the structure and function of the tight junctions of the epithelial lining; these junctions are what allow different things to pass through the gut lining.

Organic Acid Testing (OAT)

OAT testing is a simple urine test that can be completed from the comfort of your own home. This test captures bacterial byproducts from the intestine that can occur with dysbiosis and brings to light a variety of vitamin deficiencies that are important for overall health.

Breath Test

In some cases, practitioners may opt to run a breath test that tests for hydrogen and methane, particularly if small intestine bacterial overgrowth (SIBO) is suspected. This is another at-home test where the patient drinks a sugar solution and then breathes into a special balloon at specific times over 2 to 3 hours. The sample is tested for gasses produced by certain bacteria, and the amount of these gasses may indicate a bacterial imbalance in the upper intestine.

Other Lab Tests to Check

While the following tests do not directly identify dysbiosis, they can be helpful in some instances to get a comprehensive analysis of gut health when approaching a case from a functional medicine perspective.

  • Food sensitivity tests evaluate IgG levels to various food antigens. These tests can help guide dietary interventions for each individual. In a case of dysbiosis, an individual is more likely to develop food sensitivities, and limiting offending foods while rebalancing the microbiome is an essential part of healing. A lack of beneficial bacteria or an overgrowth of pathogenic bacteria can play a role in developing food sensitivities, and temporarily removing the foods allows the immune system to stop mounting an antibody response against those foods.
  • Mycotoxin testing if mold exposure or sensitivity is suspected: Mold and the resultant production of mycotoxins can lead to imbalances in the bacteria in the gut and can negatively impact the intestinal epithelial lining.
  • Genetic testing evaluates enzyme ability for metabolic processes like detoxification, vitamin D receptor function, and brain neurotransmitter regulation. Optimal detoxification is essential for rebalancing the gut microbiome.

Functional Medicine Treatment for Dysbiosis

Antimicrobials & Antifungals

Your practitioner may recommend an initial course of prescribed or herbal antibiotics or antifungals if your test results indicate high bacteria or fungal species levels.

If medication use is at the root of your dysbiosis, a course of antimicrobial herbs may be suggested over pharmaceuticals. It's essential to work with a practitioner to ensure you have a personalized treatment plan for your case.

Antimicrobial herbs are often used to support the rebalancing of the gut microbiome. Depending on a given clinical presentation and comprehensive stool test results, antimicrobial herbs can target specific pathogens, such as candida overgrowth or parasites. Many herbs have shown to be just as effective as prescription antibiotics in studies.

Performing follow-up lab tests to evaluate the efficacy of antimicrobials is essential and, depending on the case, should be done somewhere in the 4-12 week range.


While a nutritional approach to dysbiosis can differ from person to person based on each unique case, shifting towards an anti-inflammatory, nutrient-dense diet is a good starting place. Depending on a person's history, symptoms, and lab results, different therapeutic nutrition approaches may be used, such as an elimination diet with reintroduction or a low FODMAP diet. A Mediterranean diet rich in plant foods or a Paleo approach may be optimal for others.

A variety of plant foods provides a high polyphenol content, which can help support the growth of beneficial gut bacteria.

Opting for high-quality animal proteins, a variety of vegetables and seasonal fruits, healthy fats like avocado or olives, fish, poultry, and whole grains like oats, while minimizing refined sugar, processed meats, junk food, gluten, and refined grains is the goal of most therapeutic nutrition plans for healing dysbiosis.

While prebiotic and probiotic foods are often recommended for a healthy gut, some individuals with dysbiosis may find that consuming these foods can give them symptoms like gas or bloat. It may take some time to introduce a probiotic food (or supplement) into the diet. Some examples of probiotic and prebiotic foods include goat's or coconut yogurt, miso, oats, flax seeds, unripe bananas, seaweed, inulin, and kombucha.

Functional lab tests, including microbiome testing and food sensitivity testing, can help further personalize a nutrition approach to help restore balance to the gut.


Prebiotics and probiotics can help increase beneficial microbes in the gut. Advanced functional stool testing can help personalize probiotic recommendations by evaluating what microbes are actually in your gut. It should be noted that not everyone does well with a probiotic initially, and these supplements can cause bloating and other gastrointestinal symptoms if it's not the right fit for you.

Zinc carnosine is an effective supplement for gut repair and strengthening the gut lining while also supporting a healthy immune response.

Ginger has been shown to reduce inflammation and have a favorable effect on the diversity of microbes in the gut. Ginger is a natural prokinetic that helps improve stomach emptying and is commonly used in SIBO cases.

Vitamin D deficiency is increasingly common and has been linked to dysbiosis. Its benefits have been studied in both healthy and chronically ill populations, demonstrating improvement of dysbiosis across the board.

Lifestyle Changes

When it comes to supporting optimal gut health, simple lifestyle changes can go a long way. Eating whole foods, practicing good dental hygiene, hydrating, prioritizing sleep, incorporating regular exercise, and swapping out personal care products and cleaning products for non-toxic versions are all important lifestyle habits that can support a healthy gut.

Additionally, learning how to manage stress effectively is an important component of rebalancing the gut microbiome. Yoga, exercise, and meditation are all activities that can help reduce stress and support healing.

Fecal Microbiome Transplant

Fecal microbiome transplantation (FMT) has gained popularity as a potential treatment option for severe gut imbalances in recent years. It is most commonly performed as a treatment for recurrent C. difficile colitis. C. difficile colitis, is a complication of antibiotic therapy.

In an FMT, fecal material from a healthy individual is transferred directly to the person with a compromised gut function to help beneficial microbes repopulate upon transfer.


Dysbiosis is an increasingly common gut condition that can contribute to various chronic inflammatory illnesses in affected individuals. A thorough history and functional medicine evaluation can help determine if dysbiosis is contributing to your symptoms and help guide the best therapeutic plan for rebalancing the microbiome based on your unique case. A combination of nutrition, lifestyle interventions, and targeted supplements can help rebalance the gut and strengthen this important foundational piece of optimal health and well-being.

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The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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