Gutbliss - Dr. Robynne Chutkan



Dysbiosis is an alteration of your body’s microbial community that diminishes your essential population of good bacteria and allows pathogenic (bad) bacteria that are normally present in low amounts to flourish. A high-fat, high-sugar/low-fiber diet, excessive alcohol, medications like acid blocking proton pump inhibitors (PPIs), non-steroidal anti-inflammatory drugs (NSAIDs), and many others can all cause dysbiosis. Vaginal yeast infections or thrush in the mouth after a round of antibiotics is an example of localized dysbiosis—the native yeast population proliferates after the antibiotics destroy large numbers of essential bacteria. Other forms of dysbiosis include small intestine bacterial overgrowth (SIBO) and bacterial vaginosis (BV). Severe dysbiosis may manifest as more serious disease that can affect the entire body and is felt to be part of the root cause of some autoimmune conditions.


Clinical manifestations of dysbiosis vary tremendously from person to person and may include:

  • Acne, eczema, rosacea
  • Allergies and chronic food sensitivities
  • Bad breath and gum disease
  • Bloating or foul-smelling gas
  • Brain fog
  • Candida overgrowth or chronic yeast problems
  • Chronic unexplained fatigue
  • Depression or anxiety
  • Difficulty losing weight
  • Frequent colds, flu, or sinus infections
  • Mucus in stool
  • Itchy ears
  • Burning sensation in the mouth
  • Poor digestion including acid reflux
  • Stomach bugs or episodes of food poisoning
  • Unexplained diarrhea
  • Vaginal itching and/or discharge
  • Anal itching

Associated Conditions

Because microbes are integrally involved in most of our bodily functions, scientists are finding that microbial imbalance is the driving force behind many new and existing disorders. While alterations in the microbiome may not be the only cause of these disorders, dysbiosis often plays a central role, and rebalancing gut microbes frequently leads to a significant improvement in symptoms. The following are conditions that are common people with dysbiosis:

  • Autoimmune disease
  • Bacterial vaginosis (BV)
  • Bloating
  • Celiac/gluten sensitivity
  • Chronic fatigue syndrome (CFS)
  • Depression
  • Diabetes
  • Food allergies and sensitivities
  • Food cravings
  • Inflammatory bowel disease (IBD)
  • Irritable bowel syndrome (IBS)
  • Leaky gut
  • Multiple sclerosis
  • Obesity
  • Parasites
  • Sinusitis
  • Skin conditions (acne, rosacea, eczema)
  • Small intestinal bacterial overgrowth (SIBO)
  • Thyroid disease
  • Weight gain
  • Yeast overgrowth


Dysbiosis is usually caused by a combination of factors (food and drink, daily medications, and stress, for example) that ultimately tip people over the edge and create symptoms. Many people with dysbiosis have a history of excessive antibiotic use at some point in their lives. Whatever it may be, identifying and remediating the cause of bacterial imbalance is an essential step in the treatment of dysbiosis. Below is a list of some of the medications and conditions that can disrupt your intestinal balance and cause dysbiosis:

  • Acid suppressing drugs (PPIs)
  • Alcohol
  • Antibiotics
  • Artificial sweeteners
  • Birth control pills
  • Bowel obstruction
  • Chemotherapy
  • Constipation
  • Crohn’s disease
  • Decreased motility
  • Diabetes
  • Diverticulosis
  • Fatty foods
  • Fistulas
  • Gastric bypass surgery
  • Hormone therapy
  • Hypochlorhydria (low acid)
  • Hypothyroidism
  • Immune deficiency
  • Infections
  • Low fiber
  • NSAIDs
  • Pancreatic enzyme deficiency
  • Parasites
  • Post-operative changes
  • Scleroderma
  • Steroids
  • Stress
  • Sugar over-consumption


Because you can’t see or touch dysbiosis like most digestive diseases, mainstream medicine is only now beginning to recognize it as a real condition, even though millions of Americans suffer from it. For these reasons, dysbiosis can be a challenging diagnosis to make. There are tests that may provide supporting evidence, but many are not clinically validated, so dysbiosis is primarily a clinical diagnosis. Some of the tests include:

Microbiome testing: using swabs from stool, the microbiome is sequenced and analyzed for indications of bacterial imbalance, including elevated levels of certain families of bacteria and reduced amounts of others. 

Breath hydrogen tests: used to test for dysbiosis in the small intestines, or SIBO. Glucose is consumed and levels of hydrogen in the breath are tested. Pathogenic bacteria break down glucose and release hydrogen gases, and therefore elevated levels of hydrogen infer possible dysbiosis.

Candida testing: includes blood tests for IgG, IgA, and IgM, antibodies to candida and a urine test that detects waste products of candida. 

Dysbiosis is primarily a clinical diagnosis based on careful history taking (including a close look at lifestyle habits and personal history), and familiarity with the spectrum of disorders that can result from damage to the microbiome. This is often the only way to make an accurate clinical diagnosis. Whether you’ve already been diagnosed with dysbiosis or one of its associated conditions or are still trying to figure out the cause of your symptoms, the questions below will help you identify whether dysbiosis may be the root cause(s) of your digestive distress.

Risk Factors for Dysbiosis:

  • Have you taken antibiotics more than four times per year or for longer than two weeks at a time?
  • Have you been on birth control pills or hormone replacement therapy in the last 5 years?
  • Have you taken corticosteroids such as prednisone or cortisone for longer than two weeks at a time?
  • Have you been on acid suppressive therapy with proton pump inhibitors (PPIs) for more than two months at a time?
  • Do you take ibuprofen, aspirin or other NSAIDs regularly?
  • Were you a picky eater growing up (or currently) who rarely ate green vegetables?
  • Have you consumed large amounts of sugar and starchy foods?
  • Do you drink more than ten alcoholic beverages per week?
  • Do you drink one or more sodas or diet sodas daily?
  • Have you ever had diarrhea or dysentery with foreign travel?
  • Have you ever been diagnosed with a parasite?



Many doctors prescribe antibiotics for dysbiosis, as well as for dysbiosis-related symptoms, including bacterial vaginosis (BV), cystic acne, and recurrent sinus infections, but this approach is part of the problem, not the solution. Antibiotics may temporarily improve your symptoms, but for most people it’s a shortsighted fix, making things worse in the long term, as antibiotics kill off large amounts of essential good bacteria. Your symptoms may initially get better since the antibiotics wipe out both good and bad bacteria, but a vicious cycle of recurring symptoms/more antibiotics is likely to occur because of the antibiotic-induced bacterial disruption.

The Gutbliss 3-Pronged Approach: Remove, Replace, Restore (“Live Dirty, Eat Clean”)

“Rewilding” means the reintroduction of species into areas where they’ve become extinct, with the goal of returning to a more natural and balanced existence. It’s an important part of repairing and restoring our relationship with the natural world—not just the one we live in but also the one that lives inside us. Just as conservation efforts of reforestation, protecting wildlife, and replenishing the oceans are essential to life on the planet, so re-creating a balanced microbial habitat in our bodies might be the single most important step in improving our individual and collective health. But how exactly do we rewild ourselves? What do we need to do to restore and maintain a densely populated, healthy microbiome, with the right mix of species all working together? 

Treating dysbiosis can be complex and highly individualized. The Gutbliss 3-Pronged Approach has proven successful in many individuals suffering from dysbiosis. The cornerstone of this method developed by Dr. Robynne Chutkan (and popularized in her 2nd book The Microbiome Solution), is removing medications, practices, and foods that are damaging to your microbiome; replacing the essential bacteria that you’ve lost with exposure to soil microbes – and when appropriate, a robust probiotic; and restoring the health of your gut with appropriate nutrients and medicinal foods.

  • Remove antibiotics and other drugs that contribute to the problem, including acid suppressors, NSAIDs, birth control pills, hormone therapy, steroids etc. Avoid household and personal care products that disrupt the microbiome.
  • Replace your depleted gut (or vaginal) microbes through exposure to soil microbes in nature, and with live bacteria in the form of a robust probiotic when appropriate.
  • Restore the growth of good bacteria by consuming prebiotics found in high-fiber foods that feed your good bugs, including foods such as oats, artichokes, asparagus, garlic, onions, and leeks, and fermented foods such as sauerkraut and kimchi that increase the number of good bacteria. Stay away from sugary, starchy foods that favor proliferation of bad bacteria which thrive on sugar. 

It may take several months before you see meaningful results, but this approach offers the possibility of a real cure. It took a lifetime to build your microbiome and getting it back to a state of balance is a gradual process, but with the approach outlined above, tangible improvements can almost always be made.

Dr Chutkan’s call to action for this rewilding approach to dysbiosis that aims to improve the diversity and balance of the microbiome is: “Live Dirty, Eat Clean”.

The Live Dirty, Eat Clean Diet is a whole new way of looking at food that emphasizes the nutrients you need to grow a good gut garden. It combines the best of how our Paleolithic ancestors ate with microbe-boosting, plant-based strategies, and it has helped thousands of people with dysbiosis and autoimmune diseases like Crohn’s and ulcerative colitis recover and heal. Using food as the nourishing medicine that it’s meant to be will optimize your microbiome, help you achieve and maintain your ideal weight, boost your energy levels, and improve your overall health. It incorporates: 

  • Lots of high-fiber plant matter in the form of fresh vegetables and fruits
  • Microbe-boosting whole grains and legumes that contain food for our microbes to eat
  • The option of a small amount of high-quality protein and fat from animal sources

Here are ten tips for how to approach the diet:

  • #1: Choose your carbs carefully; focus on resistant starches and inulin
  • #2: Eat lots of fermented food like sauerkraut and kimchi
  • #3: Manage your meat intake – not more than one animal daily
  • #4: Eat more plants!
  • #5: Choose food with dirt on it that has been grown in soil, not a factory
  • #6: Say no to sugar
  • #7: Focus on adding in healthy foods to crowd out unhealthy foods.
  • #8: Retrain your taste buds to go for more bitter vegetables in place of sugary desserts
  • #9: Eliminate Franken foods and eat more whole foods
  • #10: Follow the 1-2-3 Rule; consume one vegetable for breakfast, two for lunch, and three for dinner

For detailed information on the diet, as well as a list of specific foods to eat and what foods to avoid, meal plans, and recipes, check out Dr Chutkan’s 2nd book, The Microbiome Solution.

Remove medications, practices, and foods that are damaging to your microbiome, replace essential bacteria, and restore the health of your gut with appropriate nutrients and medicinal foods.


Dr Robynne Chutkan
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