In approximately 75% of new patients who see Dr. Chutkan and who have been previously diagnosed with acid reflux, after a detailed health history investigation and testing, the underlying cause of reflux symptoms is Small Intestinal Bacterial Overgrowth (SIBO), and not acid reflux.


Acid reflux happens when the valve between the esophagus and stomach, that should be shut tight when food isn’t passing into the stomach, opens inappropriately, allowing partially digested food and acid to enter the esophagus. In infants, the valve between the esophagus and stomach sometimes isn’t fully functional at birth, which can lead to acid refluxing up from the stomach into the esophagus, causing heartburn and spit up after eating.

Reflux in adults, children, and infants may develop into a more serious condition known as gastroesophageal reflux disease or GERD. GERD is characterized by chronic reflux symptoms and/or esophageal tissue damage due to recurring exposure to stomach contents, including food particles and stomach acid. Although GERD does not always lead to more serious complications, it can be a precursor for esophagitis and Barret’s esophagus.

In approximately 75% of new patients who see Dr. Chutkan and who have been previously diagnosed with acid reflux, after a detailed health history investigation and testing, the underlying cause of reflux symptoms are SIBO, and not acid reflux.


Symptoms of reflux include:

  • Heartburn
  • Regurgitation of food and/or stomach acid
  • Sour or bitter taste in the mouth
  • Burping
  • Post-meal nausea
  • Bloating
  • Upper abdominal pain

Symptoms of GERD include:

  • Asthma
  • Bad breath
  • Chest pain/discomfort
  • Chronic cough
  • Earaches
  • Excess saliva
  • Hoarseness
  • Laryngitis
  • Lump in the throat feeling

Symptoms of reflux/GERD in Children & Infants include:

  • Abdominal pain
  • Cough
  • Crying during or after eating
  • Difficulty eating often accompanied by choking and/or gagging
  • Eating strike
  • Gas
  • Heartburn
  • Vomiting

Causes of reflux/GERD include:

  • Overweight
  • Smoking
  • Caffeine
  • Alcohol
  • Consuming large meals at night
  • Stress (it increases stomach acid production, causing heartburn and nausea)
  • Intense exercise for long periods of time
  • Pregnancy
  • Gastroparesis
  • Stomach cancer
  • SIBO (or Dysbiosis)
  • H. pylori eradication

Causes of reflux and GERD in infants are often due to a digestive system that is not fully developed. In infants, the valve between the esophagus and stomach sometimes isn’t fully functional at birth, which causes the valve to open and allows stomach contents to backflow into the esophagus.


Non-complicated reflux is usually a clinical diagnosis based on typical reflux symptoms such as burping, regurgitation, and chronic heartburn. If you believe you may have GERD and are experiencing more serious symptoms, your doctor may recommend the following tests:

SIBO (or BOSI) breath test: as mentioned, a large percentage of patients diagnosed with reflux actually have SIBO, and the bacterial imbalance in the gut causes gas production and in turn, reflux. If you have been on medication for your reflux or have been suffering for reflux for some time with no solution, taking a breath test is recommended.

Barium swallow radiograph: a solution containing barium (which highlights areas of inflammation or damage) is consumed and x-ray pictures are taken of the upper GI tract to investigate damage due to reflux

Endoscopy/EGD: a small tube with a camera on its end, called an endoscope, is inserted through the mouth and is used to look at the esophagus, stomach, and small intestine to detect physical manifestations of reflux damage

Esophageal manometry: a flexible tube, or catheter, is inserted into the nose and down into the esophagus and stomach. The test is used to measure esophageal functionality, which can offer insight into what’s causing your reflux/GERD

Esophageal impedance monitoring: a monitoring test, which utilizes electrical currents to measure how the esophagus functions as food passes through, offering information about how the esophagus is contributing (or not contributing) to your reflux

pH monitoring: a capsule is placed at the base of the esophagus, using an endoscope, which transmits information to a monitor worn on the waist. The test measures the amount of pH and/or the amount of acid backflow into the esophagus in a 24-hour period

Keep in mind that the barium swallow and EGD are tests that look for alterations in the esophageal tissue caused by damage from stomach contents, yet in many reflux and GERD patients no tissue alterations occur. Therefore, these tests are not a definitive way to confirm or deny a diagnosis of reflux or GERD.

Because large polyps, either benign or cancerous (although larger polyps are more likely to become cancerous), may become inflamed and bleed, stool tests that look for blood in the stool can help in diagnosing polyps. If the result of a stool test is positive for blood in the stool, a colonoscopy is recommended for further investigation.



Acid-blocking drugs are the most common treatment for reflux and GERD and include: over-the-counter antacids, H2 receptor antagonists, and proton pump inhibitors (PPIs). These medications might bring relief, but it comes at a hefty price, putting you at risk for the following complications:

Dysbiosis: Stomach acid is one of our main defenses against undesirable bacteria that enters the body through the mouth. Acid-blocking drugs transform the normally inhospitable acidic environment of the stomach into a friendly place for bacteria to grow and multiply, potentially throwing off your microbial balance and causing dysbiosis.
Digestive distress: Acid-blocking drugs can also lead to overgrowth of undesirable bacteria in the small intestine, causing symptoms of gas, bloating, and belching that can mimic the signs of acid reflux in someone who’s already being treated – a classic example of how pharmaceutical intervention for one problem can actually create disease elsewhere.

Nutrient malabsorption: Acid-blocking drugs, prescribed for reflux can decrease the absorption of nutrients, including fat-soluble vitamins important for healthy skin.
Interference with digestive enzymes: They can render digestive enzymes less effective, so you may have poor digestion of protein and fat, causing lackluster skin and hair.

The Gutbliss 3-Pronged Approach

Because many cases of diagnosed reflux are actually SIBO with reflux-like symptoms, taking the appropriate steps to restore gut bacteria imbalance is recommended: remove medications, practices, and foods that are damaging to your microbiome; replace the essential bacteria that you’ve lost with a robust probiotic; and restore the health of your gut with appropriate nutrients, supplements, and medicinal foods. For more information on this approach and a step-by-step guide to rehabbing the microbiome, read Dr. Chutkan’s book, The Microbiome Solution.

Lifestyle Interventions for Adults & Children

Lifestyle modifications are the most effective way to improve reflux and GERD, while still promoting a healthy microbiome. Try these lifestyle adjustments to treat your reflux symptoms:

  • Eat five to seven small meals each day to avoid overfilling your stomach.
  • Exercise.
  • Adopt a gluten free diet.
  • Eat before sunset or shortly thereafter – your stomach literally sleeps when the sun sets.
  • Enjoy your largest meal at breakfast and your smallest meal at dinner.
  • Chew your food well.
  • Limit and split high-fiber foods throughout the day to avoid getting too full.
  • Avoid fatty foods, fried foods, dairy, caffeine, chocolate, carbonated beverages, and nicotine – they can slow down the emptying of your stomach, and/or cause the valve between your esophagus and stomach to open inappropriately, leading to reflux symptoms.
  • Be mindful of chewing gum, spicy foods, citrus, mint, onions, garlic, alcohol, and even decaffeinated teas, as these choices can exacerbate the symptoms for some.
  • Stay hydrated. Drink between meals instead of with meals and take frequent, small sips so you don’t get too full.
  • Finish eating four hours before bedtime/lying down.
  • Move after eating; take a quick walk around the block to get your stomach moving.
  • Wait a few hours after eating to exercise in order to give your stomach time to empty.
  • Wear clothes that are not tight around your waist and abdomen.

Treatment for Infants

Usually the simplest and most effective treatment for reflux is to give your baby small frequent feedings, and keep them upright for at least an hour after.

Unfortunately, parents are often given prescriptions for acid suppression medications instead – a particularly egregious practice in babies, whose precious microbes are just blossoming. Those kids often experience upper respiratory tract infections, which lead to antibiotics on top of the acid suppression, setting them up for a lifetime of problems. Be absolutely vigilant about researching and questioning every recommended pharmaceutical intervention for you and your family, and not assume that the outcome will be better health.