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gut dysbiosis

Gut Dysbiosis Causes, Symptoms, Testing, and Treatment

Gut dysbiosis means there’s an imbalance between good and bad microbes. This imbalance can lead to irritable bowel syndrome (IBS), constipation, diarrhea, gastritis, colitis, and other conditions you may have not linked to your digestive tract like fibromyalgia and autoimmune diseases. This article talks about dysbiosis causes, symptoms, how to test for dysbiosis, and how to heal gut dysbiosis.

What are the Benefits of Good Gut Bacteria?

Microflora, sometimes called microbiota, refers to the bacteria, fungus, and viruses that live in your body. There are 10 to 100 trillion microbial cells in your body made of 500 to 1,000 different species. While the majority of them reside in the gut (hence the emphasis on gut microflora) they also live in the mouth, skin, genitals, and any mucus membranes. Microbiome refers to the genetic material of these organisms.

Your microbiota and your human cells are living in a symbiotic relationship. Your body provides the habitat and food, and they do important functions for you.

Gut microbiota:

  • Helps us extract nutrients and energy from food
  • Produce vitamins like vitamin K and absorb minerals
  • Digest fiber since we don’t have the enzymes to break it down. As a result, they produce short chain fatty acids (SCFA) that nourish and strengthen the cells that line the intestine
  • Help with detoxification  
  • Is part of our immune system, helping us fight pathogens and foreign invaders
  • Maintain the integrity of the intestinal lining, preventing intestinal permeability or leaky gut
  • Participate in balancing hormones, including estrogen
  • Maintain healthy gut motility

Low microbial diversity has been linked to inflammatory bowel disease (IBD) like Crohn’s or colitis. Imbalances in gut microbiota are also linked to asthma, autoimmune diseases, eczema, autism, celiac diseases, anxiety, resistance to antibiotics, type 2 diabetes, obesity, heart disease, and cancer.

What is Gut Dysbiosis?

Gut dysbiosis means that there’s an imbalance between good and bad bacteria and other microbes in your gut. There are 3 types of dysbiosis:

  1. Not enough good bacteria to protect you from disease-causing microbes, modulate the immune system, nourish the cells of the intestine, and do their other functions
  2. Presence or large proportion of bad pathogenic bacteria, fungus, virus, or parasites that lead to disease or inflammation. These may include E coli, H Pylori, clostridia, giardia, candida, and others.
  3. Overgrowth of bacteria in the small intestine, a condition known as small intestinal bacterial overgrowth (SIBO).  The small intestine is where digestion and absorption of nutrients happen, and overgrowth of bacteria there interferes with these important functions. SIBO may be the underlying cause for up to 70% of IBS cases. (1)

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Gut Dysbiosis Causes

A few different components affect the number of microbial cells in your gut and the diversity.

  • Birth (vaginal vs c-section)

When babies are born vaginally, they are exposed to the mom’s vaginal microflora, which leads to normal “seeding” of the baby’s gut microflora and development of healthy immune system. The GI tract of babies born vaginally are initially colonized with good lactobacillus bacteria, whereas c-section babies tend to have more of the pathogenic bacteria found on the skin and in hospitals. C-section babies are at an increased risk for developing asthma, allergic rhinitis, gastroenteritis, celiac disease, and type 1 diabetes. (2)

  • Breastfeeding

Breast-fed babies get a third of their gut bacteria from their mom’s breast milk and an additional 10% from their mom’s breast skin. The more babies nurse, they more their gut flora resembles their mother’s breast milk. (3) Breastfeeding helps Bifidobacteria to colonize the baby’s gut, whereas exclusively formula-fed babies tend to have more E. coli and clostridia bacteria (pathogenic) in addition to Bifidobacteria. (4)

Your gut health is related to your mother’s. And if you’re a woman, your gut health and microbial diversity will affect your child(ren).

  • Antibiotic use during infancy

Antibiotic use during infancy leads to dysbiosis and affects the diversity and stability of gut microbiota. (5) Antibiotics increase the risk for immune, inflammatory, and metabolic diseases such as inflammatory bowel disease, asthma, allergies, autism, type 1 and type 2 diabetes, and obesity. Babies exposed to antibiotics tend to have more antibiotic-resistance genes.

  • Antibiotic exposure

While antibiotics are necessary to defeat certain bacterial infections that pose a critical risk to human health, their use excessively and without paying attention to restoring gut flora leads to serious implications. Antibiotics reduce the diversity of your gut flora, causes disruptions in your immune function (leading to weakened immunity against pathogens and autoimmunity towards your own cells), increase antibiotic-resistance, and interfere with metabolism and insulin sensitivity. (6)That’s why you see a study almost every day linking gut flora to a disease or health conditions like Crohn’s disease, diabetes, cardiovascular disease, or others! If you tend to experience yeast overgrowth (women often report vaginal yeast overgrowth) when you take an antibiotic, that’s a sign that your gut flora is weak and in dysbiosis.

  • Diet

What you eat will affect your gut microbiota. Diets high in total fat (more than 45% of calories) tend to increase bacteria that may affect human health negatively. (7)  Diets higher in monounsaturated fats (olive and avocado) and omega-3 fatty acids increase beneficial lactobacillus and bifidobacteria. (7) When it comes to polyunsaturated fats, it’s important to make the distinction between beneficial omega-6 and harmful inflammatory omega-6 fats that come from commercially processed plant oils (corn, cottonseed, soy, etc) tend to shift the balance towards harmful bacteria. While most studies find that saturated fats negatively affect your gut microbiota, one study found that unsaturated omega-6 fats are actually worse for your tight junctions that maintain intestinal lining integrity. (8) Want to know which fats to eat? Read the gut dysbiosis treatment section.  

Diets high in sugar without enough enough fiber lead to dysbiosis. Too much sucrose, glucose, fructose, as well as artificial sweeteners are harmful for microbial balance. (7) Breads, pastries, and all starches eventually get broken down to glucose and increase the sugar load in your body, and foods made with high fructose corn syrup and other syrups feed gut pathogens. While antioxidants from vegetables and fruit may not affect dysbiosis directly, they do reduce inflammatory compounds in the gut produced by harmful bacteria.  

You have 100% control of what you eat. Diet is where you can significantly tip the scale towards healing dysbiosis and preventing conditions related to it.


  • Gut motility and digestion problems

Your digestive system contracts to push food downstream for digestion, then it contracts again when you’re fasting in between meals to clean up waste, bacteria, and undigested foods. Disruptions in gut motility will promote dysbiosis because pathogens start to feed these undigested food particles. I’ve talked about grazing, MMC, and SIBO previously.

Other problems in digestion include the fact that we produce less digestive enzymes as we age, low HCL production due to PPI and other antacids use, reduced bile release due to liver or gall bladder issues or removal.

To completely get rid of your pain and discomfort and prevent long term consequences of dysbiosis, you have to restore digestion and healthy gut motility. In addition to helping my clients choose better foods to heal and repair their gut, these two steps must be addressed correctly and in the right order to get lasting results. You can read more about my complete program here.

  • Stress

Stress will turn on your parasympathetic nervous system that triggers a fight-or-flight response. This is beneficial during acute stress as your body will pump more blood to your muscles, heart, and pupils so you can become more alert and survive the danger that got in front of you. Your muscles tensing up and your heart racing after barely escaping a car accident is your parasympathetic nervous system at work. This response will also reduce blood flow to non-critical parts of your body like your gut, reduce acid production from the stomach, and slow down gut motility contractions. (9) While that’s beneficial in times of acute short-lived stress, unfortunately, many of us are dealing with chronic stress that doesn’t go away. When digestion is low and slow consistently, it will lead to dysbiosis, especially SIBO.

Most people associate stress with outside factors like work, school, social commitments, finances, and relationships, but stress can also be internal and physiological. Fluctuations in blood sugar, processed foods, chronic hidden gut infections, heavy metal toxicity, and mold exposure are also sources of stress. It’s important to identify the source of stress and eliminate it. You will improve your digestive symptoms as you manage your stress, but from my clinical practice, I find that once dysbiosis occurs, removing the source of stress alone is not enough. At some point, to reverse the damage and repair the gut, you do need a complete diet and supplement plan along with lifestyle skills like meditation, breathing, and therapy.

  • Infectious gastroenteritis

Gastroenteritis, casually known as the stomach flu, can lead to dysbiosis even after the initial acute phase of nausea and vomiting disappears. Gastroenteritis is caused by bacteria or virus after exposure from water, food, or contact from someone infected (changing diapers, touching public bathroom door knobs or faucets, etc). Most people and doctors consider the stomach flu as passing 24-hour disruption to normal life. However,  people with a less than optimal gut microbiota, weakened immune system, or people predisposed to autoimmunity may take a long term hit.

Certain viruses, parasites, or bacteria can trigger a dysfunction in the ileocecal valve, the region that separates the small from the large intestine, and trigger SIBO. Microbes such as Campylobacter, salmonella, giardia, E. coli, or viruses produce a toxin known as cytolethal distending toxin (CDT) that damages the interstitial cells of cajal (ICC). These cells are considered the pacemaker of your gut. (10) They connect the nerve cells of the intestine with the smooth muscle cells of the intestine through electric waves and trigger the muscle contractions responsible for peristalsis (digestion) and the MMC (cleaning up). Exposure to CDT triggers your immune system to produce antibodies that attack your own ICC. (11) If you started to experience reflux, bloating, stomach pain, diarrhea, or constipation after an incident of food poisoning or the stomach flu, or if you’ve been told that you have post-infectious IBS, it’s almost guaranteed that you have dysbiosis and potentially an autoimmune attack in your intestines.

Gut Dysbiosis Symptoms

How do you know if you have gut dysbiosis? There isn’t an official medical checklist or criteria for diagnosing gut dysbiosis yet. Your doctor may not even believe in it! However, how you feel may give you a hint that you may have an imbalance in your gut microflora, especially if some of the causes I just discussed apply to you. Here’s a list of gut dysbiosis symptoms. If you nod your head as you go through the list, it’s going to be very important to investigate further with proper testing.

    • Frequent gas, bloating, an/or cramping
    • Loose stool, urgency, diarrhea
    • Constipation
    • Cycling between diarrhea and constipation
    • Diagnosis of Irritable Bowel Syndrome (IBS) (IBS-C, IBS-D, post-infectious IBS)
    • Mucus in your stool
    • Acid reflux, GERD, or if you’ve used a PPI for an extended period of time
    • Silent acid reflux, LPR
    • Chronic bad breath
    • Diagnosis of inflammatory bowel disease (IBD) such as Crohn’s and colitis
    • Feeling full quickly after meals, even with small amounts, no matter what you eat
    • Fatigue or low energy
    • Joint and muscle pain
    • Sinus congestion
    • Chronic headaches and migraines
    • Brain fog, anxiety, and/or depression
    • Food sensitivities and allergies
    • Asthma and environmental allergies
    • Nutrient deficiencies like iron, vitamin D, vitamin B12
    • Carbohydrate intolerance, not being able to tolerate starchy or fiber foods
    • Autoimmunity, or an autoimmune condition such as Hashimoto’s thyroiditis, psoriasis, RA, multiple sclerosis
    • Histamine intolerance symptoms such as rashes, headache, stomach pain, sinus issues
    • History of stomach flu, gastroenteritis, and/or food poisoning
    • History of prolonged antibiotics use such as for acne or sinusitis


Learn how to identify the REAL causes of your gut problems.

Download My Free Guide.

Gut Dysbiosis Tests

While a colonoscopy and an endoscopy can help you rule out celiac disease, IBD, obstruction, and cancers, they will not diagnose dysbiosis. From clinical practice, I find that the best diagnostic tools for identifying dysbiosis are breath testing for SIBO, microscopic (not culture) stool tests that identify microbial genetic material, as well as organic acid urine test. Apply for a strategy session call to learn more about these tests and how they can help you identify your specific gut dysbiosis type and root causes.

Why is It Important to Heal Gut Dysbiosis?

It’s important to heal and reverse gut dysbiosis to prevent these 6 health problems:

  1. Autoimmune diseases. Dysbiosis is one of the risk factors and triggers of autoimmunity. (12) Once you have an autoimmune disease, it cannot be reversed or cured, but it can be managed or put into remission with changing the diet and addressing the root causes. Unfortunately, many people live with painful and disruptive autoimmune conditions, especially Hashimoto’s, for years before getting a diagnosis. Others sadly live a lifetime with autoimmune conditions not knowing the connection to the gut and that they can reduce their pain with the right diet and gut healing protocol.
  2. Inflammatory bowel disease (IBD). Crohn’s disease and colitis are two inflammatory bowel diseases that are a combination of a hyperactive immune system and autoimmunity. Both can lead to severe pain, blood in stool, nutrient deficiencies, and may result in surgical removal of parts of the intestine. You can’t be cured from an IBD, you can only put your condition into remission, and that’s why prevention is key.
  3. Estrogen hormone imbalance. A group of microbes in your gut known as estrobolome participate in balancing estrogen metabolism and detoxification. Dysbiosis increases free estrogen circulating in your body, which activates estrogen receptors and increases estrogen-related conditions such as PMS, obesity, osteoporosis, heart disease, endometriosis, PCOS, as well as cancer estrogen-dependent cancers. (13)
  4. Neurological and psychiatric conditions. Gut dysbiosis has been linked to several mental health, neurologic and psychiatric conditions such anxiety, depression, ADD/ADHD, autism, Parkinson’s disease, and age-related cognitive decline. (14, 15, 16)
  5. Cancers. Gut dysbiosis has been linked to cancers of the stomach, esophagus, estrogen-related cancers, colorectal cancer, and others. In addition, healthy gut flora and probiotics can improve cancer treatments and outcomes. (17, 18)
  6. Metabolic syndrome. Gut dysbiosis has been linked to obesity, type 2 diabetes, and heart disease, which are preventable chronic conditions and leading causes of deaths in the US and worldwide.

Gut dysbiosis can be very painful, uncomfortable, and ultimately lead to more serious complications that affect the quality and length of your life. There’s hope, but only if you identify your root causes and calm your gut inflammation the right way!


Gut Dysbiosis Treatment

The best gut dysbiosis treatment is going to depend on the type of dysbiosis you have. If you are dealing with diarrhea or stomach pain for example, it’s possible that you have SIBO, H Pylori, clostridia, yeast, or something else. It’s important to identify the pathogen that is present or out of balance so you can narrow down the treatment options. It’s also important to identify root causes such as gut motility, stress, medications use, and either support normal function or eliminate the source of the root cause.

Dysbiosis can be difficult to diagnose and harder to fix. Unfortunately, some doctors do not believe in gut dysbiosis and its ability to affect many health conditions and symptoms. Conventional doctors may not connect your rheumatoid arthritis, Hashimoto’s, anxiety, or psoriasis to your gut microflora. If your condition is gut-related, such as IBS symptoms, IBD, H Pylori or SIBO, your gastroenterologist’s treatment options will typically be limited to pharmaceuticals, such as antibiotics, PPIs, or steroid medications. You can repair the gut and heal gut dysbiosis holistically, but you must address the many angles of a properly functioning gut. That’s why I designed my comprehensive gut repair program.

(Disclaimer: this article is for educational purposes and doesn’t replace individualized medical help, and you should always talk to your doctor before adding or stopping a medication.

My patients come to me because they want a food and nutrient-based option to support their immune system, balance their gut flora, and get rid of their pain and discomfort. They are not being offered the tests that identify dysbiosis, and treatment plans barely touch on the effect of your daily food choices that you have 100% control over. If you want to explore how I can help you identify your gut dysbiosis root causes and design a custom food and nutrient healing plan, apply for a strategy session call to map out your fastest path to recovery and thriving. Meanwhile, here are 4 things you can start doing today to improve your gut flora health and prevent or reduce your risk of gut dysbiosis:

  1. Clean up your diet. Remove sugar, commercial foods, trans fats, commercial oils, desserts, and chemicals from your diet. The topic of fats is extremely complicated to discuss here, but my general tips is to stick to a moderate amount of fats (about 35% calories) from olives, avocado, omega-3 fatty fish, pasture-fed eggs, nuts and seeds. Grass-fed red meats 2 to 3 times a week should be ok. Avoid trans fats and foods made with soybean, cottonseed, corn, or vegetable oils at all costs.
  2. Eat foods high in total fiber, especially prebiotic fiber. Aim for at least 4 to 5 cups of different types vegetables; Brassica group (broccoli, cauliflower, cabbage), leafy greens (kale, spinach), red and orange veggies (tomatoes, bell peppers, squashes), and aromatics (garlic, onion, celery). Eat 2-3 servings of fruit a day, such as berries, apples, pears, oranges. If you can tolerate beans, lentils, and whole grains, add a small amount to your diet. Most therapeutic diets I use with people who already have IBS, IBD, or autoimmune conditionals eliminate legumes and grain. If you’re in maintenance or prevention phases, you may be able to add a small amount to your diet without side effects.
  3. Take probiotics. Fermented foods like kefir, yogurt, sauerkraut, and other fermented veggies (without vinegar) contain healthy live cultures that boost your gut flora. Probiotic supplements can also help reduce your symptoms and increase microbial diversity.  
  4. Manage your stress. I understand that it’s easier than done. If possible, remove the source of the stress such as a toxic relationship or toxic job. Reduce your commitments and obligations. Say “no” to things that don’t align with your priorities and core values. Manage how you respond to stressors. Prioritize yourself and your health. Slow down and breathe. Meditate. Exercise. Book some personal self-care time. Seek help from family or friends. Work with a therapist or counselor. The list can go on and on; find something that works for your situation and your type of stress best.

No matter what you do, the sooner you address your gut dysbiosis, the easier and faster it will be to heal and thrive. You can’t control your mom’s health, diet and lifestyle choices, your genetics, whether you were vaginally born or not, breastfed or not, and whether you took antibiotics as a child or not. However, you have the ultimate control of what you choose to eat and whether you’re willing to commit to uncovering the source of dysbiosis and eliminating it. Dysbiosis is treatable and reversible, and balancing your gut microbiota will prevent serious health issues from complicating your life and wasting your health, wealth, time and energy.

Gut Dysbiosis FAQs

How can I prevent gut dysbiosis? To prevent dysbiosis, you must understand the root causes and avoid them. Use my recommendations for gut dysbiosis treatment for prevention. If you can’t do it alone, if you tried without results, or if you’re not sure how to start, I’m happy to offer a complimentary call to explain my program and tell you how I can help you.

How long does healing gut dysbiosis take? There’s no one answer that will satisfy all. With my private clients, I retest for things like SIBO, H Pylori, and other pathogens. For some patients, 8-12 weeks of gut healing diet and supplement protocol is enough to eradicate the pathogen and get a negative reading on their test. For others, it may take longer. In general, the more severe your symptoms are and the longer you’ve had them, the longer it will take to heal. That’s why I always tell people to not ignore how they feel or brush it off as normal. Being “a little” constipated or having a “sensitive” or ”silly” stomach are things people with severe dysbiosis used to say to describe their gut. The iceberg under the surface may be giant!

What is the best gut dysbiosis diet? The best long-term diet to prevent dysbiosis is going to be high in prebiotic fiber, fermented foods, vegetables (raw and cooked), small amount of fruit, moderate amount of lean proteins and healthy fats, as well as a small amount of beans and grains as tolerated. People who have dysbiosis, therapeutic diets are going to be very different. I use a variety of diets with my patients, including the low FODMAPs, SIBO, SCD, and AIP, while at the same time customizing the plan for food sensitivities.

What is the best gut dysbiosis test? From clinical practice, I find that the best diagnostic tools for identifying dysbiosis are breath testing for SIBO, microscopic (not culture) stool tests that identify microbial genetic material, as well as organic acid urine test. I offer those through my comprehensive gut repair program.

Is gut dysbiosis the same as SIBO? SIBO is one of the types of dysbiosis that accounts for up to 78% of all IBS cases. SIBO is interconnected with other digestive imbalances as it can be triggered by H Pylori, pathogenic bacteria in the large intestine, low stomach acidity, CDT toxin, motility issues, or problems with ileocecal valve. You can read more about SIBO here. I find that some cases of SIBO were a breeze to eradicate while others were more complicated and required my patient multiple protocols and therapy tools.

Which probiotic should I take? There are lots of probiotic products on the market. Some are multi-strain while other contain single strains of bacteria. Others contain beneficial yeast. Some strains are found to benefit certain conditions in research, so the best probiotic for you is going to depend on what’s going on with your health and what you’re taking it for. In general, I lean towards spore-based probiotics. If you want to purchase the product I recommend for my patients, please contact us and ask us about it.

Nour’s guidance and expertise was the key to dramatically halting our son’s [Crohn’s] disease progression! His pediatric gastroenterologist is now in agreement of our choice to treat solely with diet and supplements. All his labs have improved and his inflammatory markers are so low they are practically nonexistent.

Before working with Nour, I experienced intestinal pain off and on for for 54 years with minimal success on medications. I have benefited 100% from Nour’s program as I am now pain free!

A lot of time and money was wasted on foods that I thought would help my digestive struggles [diarrhea, bloating, hunger], but in fact I was making it worse. The main benefit is getting a handle on what negatively affects my digestive symptom. Doing a total 180 to my eating habits has been pretty amazing.