“A balanced mix with a much higher ratio of “good,” or beneficial, to “bad,” or potentially harmful, species in the microbiome is crucial for not only effective digestion, but also for overall health.”


There are more than 1,000,000,000 bacteria in each drop of fluid in the colon; this colonic bacterial environment is called the microbiome. A balanced mix with a much higher ratio of “good,” or beneficial, to “bad,” or potentially harmful, species in the microbiome is crucial for not only effective digestion, but also for overall health.

Antibiotic use, a poor diet, and other lifestyle factors, such as excessive alcohol consumption and the use of NSAIDs, are strongly associated with 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 antibiotic destroys large numbers of essential bacteria. Other types of dysbiosis include small intestine bacterial overgrowth (SIBO), vaginosis (BV), and yeast (or candida) overgrowth. Severe dysbiosis may manifest as more serious disease that can affect the entire body.

Signs & Symptoms

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 Dr. Chutkan sees most often in individuals 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
  • Sinitis
  • Skin conditions (acne, rosacea, eczema)
  • Small intestinal bacterial overgrowth (SIBO)
  • Thyroid disease
  • Weight gain
  • Yeast infection
  • 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. Yet, Dr. Chutkan finds that most patients with dysbiosis have a history of antibiotic use in excessive amounts at some point in their lives.

Whatever it may be, identifying and remediating the cause of your 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 suppressor drugs (PPIs/antacids)
  • Alcohol
  • Antibiotics
  • Artificial sweeteners
  • BCP/hormones
  • 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 dysbiosis can’t be seen or touched like most digestive diseases, mainstream medicine is only now beginning to recognize it as a real condition, despite the fact that approximately 30 million Americans suffer from it. For these reasons, dysbiosis can be a challenging diagnosis to make. There are tests that may provide supporting evidence, but they are only helpful about 50% of the time. These tests include:

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 levels of hydrogen infer possible dysbiosis

Stool analysis: a stool sample is taken and analyzed for indications of bacterial imbalance. Levels of the following markers are often investigated: good and pathogenic bacteria, cholesterol, triglycerides, long and short chain fatty acids, pH, fecal secretory IgA, Beta-glucuronidase, chymotrypsin, Iso-butyrate, N-butyrate, and Iso-valerate and N-valerate

Genova IP test for leaky gut: a non-metabolized sugar is ingested and measured in the urine to evaluate how much sugar, if any, is able to permeate through the intestinal lining

Candida testing: includes blood tests for IgG, IgA, and IgM, antibodies that respond to Candida yeast bacteria, and a urine test that detects tartaric acid, a waste product of candida

U-Biome tests X 2 (start and end): using swabs from the mouth, nose, gut, genitals, and skin, the microbiome is sequenced, offering a picture of the bacteria species that inhabit the body

Zonulin testing: circulating zonulin (a protein that regulates cellular tight junctions and therefore has implications on intestinal permeability) levels are tested in the blood; high levels infer intestinal permeability

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, this checklist will help you identify the root cause(s) of your microbiome disturbances.

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 or histamine blockers (H2 blockers) for more than a month at a time?
  • Do you take ibuprofen, aspirin or other NSAIDs regularly?
  • Were you a picky eater growing up 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, but most likely a vicious cycle of recurring symptoms/more antibiotics occurs as your bacterial balance is disrupted.

The Gutbliss 3-Pronged Approach: Avoidance, Encourage, Repopulate

Treating dysbiosis can be complex and highly individualized. Yet, the Gutbliss 3-Pronged Approach that involves Avoidance, Encouragement, and Repopulation, proves successful in many individuals suffering from dysbiosis:

  • Avoid 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.
  • Encourage 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. Staying away from sugary, starchy foods that favor proliferation of bad bacteria, which thrive on “eating” sugar, is a must. 
  • Repopulate your gut (or vagina) with large amounts of live bacteria in the form of a robust probiotic.

It may take several months, or if you have severe dysbiosis, even years before you see meaningful results, but this approach offers the possibility of a real cure. It took a lifetime to build your microbiome, therefore getting it back to a state of bliss is a gradual process, but with the Gutbliss 3-Progned Approach, tangible improvements can almost always be made.