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Acid Reflux

Small Intestinal Bacterial Overgrowth (SIBO): A Serious Complication of GERD

Aug 10, 2017

SIBO is a condition where there is overgrowth of bacteria in the small intestines. Recent research tells us that SIBO and GERD are connected and each can be a cause of other.

In a healthy human being, the small intestines do not contain too many bacteria. Bacteria are usually present inside the large intestines, where they help in absorbing certain vital nutrients, protect against disease causing microorganisms and also produce certain nutrients that benefit the host body (us!). Normal stomach acidity also plays a role in keeping bacterial populations within the small intestines in check. If there is poor stomach acidity, the small intestine loses its acid:base ratio. This allows bacteria to migrate up from the large intestine into the small intestine, which can lead to several gastrointestinal problems.

GERD is a condition caused by low stomach acid and NOT high acidity. Apart from its role in digestion, stomach acidity is also an effective deterrent for the growth and colonization of unwanted bacteria in the stomach and the small intestines. This is the perfect environment for bacteria to grow near the junction of the stomach and the small intestines.

Symptoms of SIBO

When there is an overgrowth of bacteria within the small intestines, these bacteria get access to the food that is being digested. They ferment the food and cause formation of toxic by-products along with large amounts of gas. This gas puts pressure on the lower esophageal sphincter and makes the GERD worse.

Apart From This, Other Symptoms of SIBO Are

  • Bloating
  • Diarrhea
  • Cramping and pain in the abdomen
  • Constipation (not as common as diarrhea, though)

Three Types of SIBO

Small intestinal bacterial overgrowth can be of three types, depending on the dominant gas produced by the overgrown bacteria:

Hydrogen-dominant SIBO

Hydrogen-dominant SIBO causes diarrhea in almost all the cases.

Overgrowth of hydrogen sulfide can lead to:

  • “Rotten egg” smelling flatulence and stools
  • Halitosis (bad breath)
  • Chronic fatigue syndrome
  • Brain fog and short-term memory loss
  • Diseases of the gums, among others

Methane-dominant Archaea

Methane-dominant Archaea overgrowth causes a reduction in MMC function as well as malabsorption of lactose. MMC, or migrating motor complex, are waves of electrical activity that sweep through the intestines at regular intervals (especially during fasting). They are responsible for the rumbling sound of an empty stomach. These movements help move the food and the bacteria forward through the digestive tract. When MMC function is reduced, the undigested food (and the accompanying bacteria) does not effectively move forward, leading to further fermentation of the food. It also causes heaviness of the stomach (due to delayed emptying).

Malabsorption of lactose (sugar found in milk and milk products) does not allow lactose to be broken and converted into glucose for providing energy to our body. Instead, it is fermented by bacteria to produce more gas that increases bloating and gassiness. Increased bloating exerts more pressure on the lower esophageal sphincter.

SIBO and Gerd: Double Trouble



One of the major causes of SIBO is GERD. Low stomach acidity is the common factor that links both GERD and SIBO. SIBO, in turn results in constipation and excessive gas production, both of which weaken the LES by exerting pressure on it. This makes existing GERD much worse.

Digestion is an extremely complex process and depends on a well-oiled machinery comprising of muscles, nerves and chemical messengers (neurotransmitters) and facilitators (enzymes). The food has to keep moving forward in the digestive tract and nutrients need to be absorbed from it as it passes forward to eventually create a mass of waste material. In a healthy person, when this process is working normally, bacteria also get passed along the digestive tract. But when anything goes wrong with this process, bacteria end up in places they shouldn’t be and eventually overgrow and colonize that place.

Diet also influences gut microflora. A diet that is high in refined carbs, sugars and alcohol can disrupt a healthy normal gut flora.

Complications of SIBO: Why You Should Not Allow Your GERD To Cause SIBO

Apart from making GERD even worse, there are a lot of other complications that SIBO can cause. Many of these complications can prove extremely dangerous and even life-threatening. Most overgrown bacteria produce toxic waste products that cause an inflammatory response. This can cause tissue damage and can lead to “leaky gut syndrome.” This is especially true with hydrogen sulfide overgrowth as too much hydrogen sulfide causes starving of gut cells leading to their death. This causes a break in the integrity of the gastrointestinal lining, leading to a leaky gut.

The biggest concern with SIBO is impaired digestion. Vital nutrients are not properly absorbed by the intestines leading to deficiencies of nutrients like iron, vitamins (B12, A, K, D, E), calcium, etc. Nutrient deficiencies themselves can lead to a host of other complications. For example, iron deficiency, along with a deficiency of vitamin B12, can lead to anemia, while calcium and vitamin D deficiency can lead to osteoporosis.

Chronic fatigue syndrome (CFS) is a serious complication of SIBO, especially the hydrogen sulfide type, as the gas is toxic for mitochondria. Mitochondria are the energy generating organelles within cells and when their number decreases, it could eventually lead to CFS .

RELATED: An Astonishing Case Of Chronic Fatigue: Narrated By A Professional Nutritionist

SIBO can cause inflammation of the gastrointestinal lining that may lead to ulceration. Constant inflammation can also cause cells of the lining to turn cancerous. Thus, SIBO also increases the risk of colon cancer.

How Can SIBO Be Treated?


How Can SIBO Be Treated

The treatment of SIBO rests on a three-fold strategy – to correct the underlying cause, to provide nutritional support and to treat bacterial overgrowth.

Correction Of The Underlying Cause

This requires management through diet, medication and surgery, if required. A diet that is restricted in complex carbs is required initially to cut off the nutritional source of these bacteria. Our digestive tract takes longer to digest complex carbs. The fiber part of the carbs cannot be digested by the human gut. In such a scenario, the fibers as well as the slowly digesting carbs become food for bacteria. Eliminating these complex carbs in the initial phase is key to reducing the numbers of bacteria in the small intestine. Complex carbs can then be introduced slowly, in a phased manner to build healthy bacterial populations.

A similar diet also helps restrict the growth of H. pylori, the bacterium at the root of GERD. H. pylori also feeds on fibers contained in foods loaded with complex carbs. A diet with less amounts of complex carbs will also help eliminate H. pylori. With the elimination of H. pylori, the stomach will regain its original acidity and the problem of GERD will resolve. Eventually, this also helps in treating SIBO.

Surgery is needed to correct physical anomalies that are creating an obstacle for proper movement of food along the digestive tract.

Correction Of Nutritional Deficiencies

Nutritional support should aim at correcting nutrient deficiencies due to impaired digestion and a subsequent decrease in the absorption of nutrients. Any medication that is adding to the burden of symptoms should be discontinued. This holds true for acid-blocking medication to manage acid reflux.

Eliminate Overgrowth of Bacteria

Antibiotics or alternate methods can eliminate the overgrowth of bad bacteria. Eliminating SIBO requires a broad-spectrum antibiotic (one that can act against a broad range of bacteria), which unfortunately also kills beneficial bacteria, and creating an imbalance in gut microflora. Also, antibiotic treatment does not always guarantee success and may result in recurrence of bacterial overgrowth.

Research, published in Global Advances in Health and Medicine in 2014, has tested various herbal therapies that were found equivalent to a broad spectrum antibiotic rifaximin in treating SIBO. The researchers used a variety of herbal compositions that included, among others, potent herbs like Tinospora cordifolia, dill seeds, oregano oil, sage leaves, red thyme oil, ginger, Chinese licorice and acacia.

It is advisable to supplement good bacteria with either high quality fermented foods or a probiotic supplement while treating the unwanted overgrowth of bacteria. This will help correct the microflora imbalance faster.

Please Note: With a condition like SIBO, there is an order in which imbalances need to be corrected. Functional medicine practitioners will usually first eliminate the bad bacteria, then work to correct stomach acid production, and finally re-populate the gut with the right bacteria. Rather than use a probiotic yourself, please work with a qualified practitioner to get this right and help both your GERD and SIBO.


Small intestinal bacterial overgrowth is a complex disorder to diagnose as it shares its symptoms with many other digestive problems. The relationship between SIBO and GERD is clear – GERD can cause SIBO and SIBO makes existing GERD much worse.

SIBO needs dietary and nutritional support for treatment. Dietary supplements help treat the condition and also help heal the damage done by the bacterial overgrowth.

Jitendra Rathod
Jitendra is a microbiologist and a passionate student of the human body. He is a firm believer in the power of alternative and holistic medicine. He believes nature holds the key to restore us back to health and balance.