What is dysbiosis?

Your body is full of colonies of harmless bacteria known as microbiota. Most of these bacteria have a positive effect on your health and contribute to your body’s natural processes.

But when one of these bacterial colonies is out of balance, it can lead to dysbiosis. Dysbiosis typically occurs when the bacteria in your gastrointestinal (GI) tract — which includes your stomach and intestines — become unbalanced.

Some effects of dysbiosis, such as stomach upset, are temporary and mild. In many cases, your body can correct the imbalance without treatment. But if your symptoms become more serious, you’ll need to see your doctor for diagnosis.

Read on to learn more about what can cause dysbiosis, how to recognize its symptoms, and what you can do to treat and prevent this condition.

Any interruption in the balance of microbiota can cause dysbiosis.

When dysbiosis happens in your GI tract, it’s typically the result of:

  • a dietary change that increases your intake of protein, sugar, or food additives
  • accidental chemical consumption, such as lingering pesticides on unwashed fruit
  • drinking two or more alcoholic beverages per day
  • new medications, such as antibiotics, that affect your gut flora
  • poor dental hygiene, which allows bacteria to grow out of balance in your mouth
  • high levels of stress or anxiety, which can weaken your immune system
  • unprotected sex, which can expose you to harmful bacteria

Dysbiosis is also common on your skin. It can be caused by exposure to harmful bacteria or an overgrowth of a single type of bacteria.

For example, Staphylococcus aureus bacteria can grow out of control and lead to a staph infection. Gardnerella vaginalis bacteria can overtake healthy bacteria in the vagina and cause vaginal burning, itching, and discharge.

Your symptoms will depend on where the bacteria imbalance develops. They may also vary based on the types of bacteria that are out of balance.

Common symptoms include:

  • bad breath (halitosis)
  • upset stomach
  • nausea
  • constipation
  • diarrhea
  • difficulty urinating
  • vaginal or rectal itching
  • bloating
  • chest pain
  • rash or redness
  • fatigue
  • having trouble thinking or concentrating
  • anxiety
  • depression

After going over your medical history and assessing your symptoms, your doctor may order one or several of the following diagnostic tests:

Organic acids test

Your doctor will collect a urine sample and send it to a laboratory. The lab technician will test for certain acids that bacteria can produce. If these acid levels are abnormal, it may mean that certain bacteria are out of balance.

Comprehensive digestive stool analysis (CDSA)

Your doctor will have you take home special equipment to obtain a sample of your poop. You’ll return this sample to your doctor for lab testing. The lab technician will test the poop to see what bacteria, yeasts, or fungi are present. The results can tell your doctor if there’s an imbalance or overgrowth.

Hydrogen breath test

Your doctor will have you drink a sugar solution and breathe into a special balloon. The air in the balloon can then be tested for gases produced by bacteria. Too much or too little of certain gases can indicate a bacterial imbalance. This test is often used to test for small intestinal bacterial overgrowth (SIBO).

Your doctor may also take a sample of bacteria or tissue (biopsy) from an area of an active infection to see what bacteria are causing the infection.

If medication is behind your bacterial imbalance, your doctor will likely advise you to discontinue use until the bacterial balance is restored.

Your doctor may also prescribe medications to help control the bacteria, including:

  • ciprofloxacin (Cipro), an antibiotic that treats gut infections resulting from dysbiosis
  • rifaximin (Xifaxan), an antibiotic that treats symptoms of irritable bowel syndrome (IBS), a common condition associated with dysbiosis
  • co-trimoxazole (Septrin), an antibiotic that treats gut and urinary tract infections that result from dysbiosis

If your diet is at the root of your bacterial imbalance, your doctor will help you create a nutrition plan.

This can help make sure you’re getting enough nutrients to keep bacteria in balance, including:

Your doctor may also tell you to stop eating certain foods that contain harmful chemicals or too much of certain nutrients.

Foods that you can add to your diet include:

  • dark, leafy greens, including spinach and kale
  • fish, including salmon and mackerel
  • fresh meats (avoid processed meat products)

Foods that you may need to stop eating include:

  • processed meats, such as deli meat and salted or canned meat
  • carbohydrates in corn, oats, or bread
  • some fruits, such as bananas, apples, and grapes
  • dairy, including yogurt, milk, and cheese
  • foods high in sugar, such as corn syrup, maple syrup, and raw cane sugar

Taking pre- and probiotics can also help keep your gut bacteria in balance. These supplements contain cultures of specific bacteria that you can eat, drink, or take as medications. Talk to your doctor about which types of pre- or probiotics you’ll need to keep your microbiota balanced.

Some research shows that yoga and meditation can help your body absorb nutrients. They can also increase blood flow to your brain and back to your gut. This can reduce some of the symptoms of dysbiosis.

Dysbiosis has been shown to be closely associated with certain diseases and conditions, including:

Dysbiosis is usually mild and can be treated through medication and lifestyle changes. But if left untreated, dysbiosis can lead to chronic conditions, including IBS.

See your doctor right away if you’re experiencing any unusual or persistent stomach pain or skin irritation. The sooner your doctor diagnoses your condition, the less likely you are to develop any additional complications.

Certain lifestyle changes can help maintain your bacterial balance and prevent overgrowth from occurring.


  • Only take antibiotics under your doctor’s supervision.
  • Talk to your doctor about adding a pre- or probiotic supplement to your daily routine to help regulate your gastrointestinal bacteria.
  • Drink less alcohol or avoid it altogether, as it can interrupt the balance of bacteria in your gut.
  • Brush and floss every day to prevent bacteria from growing out of control in your mouth.
  • Use condoms every time you have sex to help prevent the spread of sexually transmitted bacteria and infections.
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