SIBO and Heartburn

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Small intestine bacterial overgrowth (SIBO) and Helicobacter pylori (H. pylori) are two bacterial infections that can lead to heartburn, acid reflux, and GERD. H. pylori were previously discussed. The focus of this article will be on SIBO.

What is Small Intestine Bacterial Overgrowth (SIBO)?

The small intestine has three sections: the duodenum, jejunum, and ileum. The duodenum helps further break down food after it has gone through digestion in the stomach. The jejunum and ileum absorb nutrients from the digested food.

There are beneficial as well as unhealthy bacteria found in the intestines. Beneficial bacteria are important in the function of a healthy small intestine. Beneficial bacteria help:

  • Defend against harmful bacteria and yeast.
  • In the absorption of nutrients.
  • By producing short-chain fatty acids, folate, and vitamin K.
  • Maintain the muscular activity that keeps food moving through the intestinal tract.

SIBO occurs when the small intestine is overgrown with unhealthy bacteria.1,2 Unhealthy bacteria:

  • Slow down digestion.
  • Damage to the mucous membrane of the gastrointestinal tract. This damage can lead to a leaky gut. A condition where compromised intestines allow unwanted molecules to pass through the intestinal wall into the bloodstream. A leaky gut can lead to immune disorders.
  • Prohibit the absorption of nutrients.
  • Have a by-product of methane and hydrogen gas. This gas can cause irritable bowel syndrome (IBS), abdominal pain, intestinal cramping, abdominal bloating, belching, and flatulence.

Related Content: Helicobacter Pylori and Heartburn

How Does SIBO Cause Heartburn, Acid Reflux, and GERD?

The overgrowth of bacteria in the small intestine can cause heartburn, acid reflux, and GERD in the following three ways:1,2

  1. Gas produced by the bacteria in the small intestine can cause it to expand. This expansion pushes upward placing pressure on the stomach. Added pressure on the stomach can cause stomach contents to push against the lower esophageal sphincter (LES) and leak through (reflux) into the esophagus. The LES is the valve at the base of the esophagus that closes to keep acids in the stomach from backing up into the esophagus causing heartburn. Chronic acid reflux is GERD.
  2. Gas produced by the bacteria can travel back up to be belched out. This gas weakens the LES by causing pressure on the valve. The passing of gas through the LES during belching allows for acid reflux as well.
  3. The bacteria overgrowth leads to an inability to synthesize certain digestive enzymes, reduces the small intestine’s ability to break down proteins into amino acids, and prevents the absorption of nutrients causing a slowing of the digestive process. The slowing of the digestive process causes an increase of food in the small intestine. This increase in volume puts pressure on the stomach and thusly on the LES leading to the possibility of acid reflux, heartburn, and GERD.

What Causes SIBO?

Small intestine bacterial overgrowth can be caused by any of these factors:

1) Low Hydrochloric Acid Level

Normal hydrochloric acid (HCl) levels are beneficial in killing off harmful bacteria preventing overgrowth. If stomach acid is low, unhealthy bacteria will grow.

Low stomach acid can be caused by:

  • Certain bodily disorders or illnesses.
  • A decrease in stomach acid due to age.
  • Use of heartburn medications to relieve heartburn symptoms. Studies have shown that those who take acid reducer and blockers raise the risk of SIBO. H2 blockers raise the risk by up to 17% and PPIs raise SIBO risk by 53%.1
  • Poor or improper diet.
  • Refined sugar depletion of vitamins and minerals.
  • A lack of vitamins, minerals, and other nutrients.
  • High levels of yeast/fungi (Candida overgrowth) in the digestive tract.
  • Prescription medications.
  • Diluting of acids by drinking too much water or other liquid at meals.

2) Dietary Choices

Unhealthy bacteria feed on starches and both refined and natural sugars. Diets heavy in starches and sugars promote the growth of bacteria. A well-balanced diet will provide the nourishment needed by the digestive tract for optimal performance.

3) Intestinal Dysmotility

The intestinal tract uses muscular contractions to move contents through the digestive tract and between meals migrating motor complexes (MMC) occur to clean out residual debris and bacteria. Dysmotility occurs when the intestines lack the ability to coordinate these events as they should. Surgery, intestinal damage, disease, gastrointestinal infections, and certain drugs including antibiotics, acid reducers, and certain prescription pain medications can cause intestinal dysmotility.

4) Structural Abnormalities of the Digestive Tract

Structural abnormalities of the digestive tract can impair the intestine’s ability to clean out debris and bacteria. These structural abnormalities may be genetic or from digestive tract damage, surgeries or procedures. The intestine’s inability to clean out bacteria can allow SIBO.

5) Immune Deficiency

People who have an immune deficiency are prone to bacterial overgrowth.

6) Malfunction of the Ileocecal Valve

The ileocecal valve is the valve between the ileum (the lower section of the small intestine) and the large intestine. It closes to prevent the contents of the large intestine from backing up into the small intestine. If the valve isn’t functioning properly bacteria in the colon can travel back into the small intestine adding to the potential of SIBO.

7) Other Risk Factors

  • Alcohol use
  • Oral contraceptives
  • Antibiotics
  • Irritable bowel syndrome (IBS)
  • Celiac disease
  • Crohn’s disease
  • Diabetes
  • Renal failure
  • Cirrhosis of the liver
  • Pancreatitis

Diagnosis of SIBO

SIBO can be hard to diagnose due to its overlap with other digestive disorders such as Candida overgrowth, acid reflux/GERD, gastroparesis, and IBS. It is estimated to affect 2.5% to 22% of healthy people, while up to 90% of people with health deficiencies may have SIBO.2 To determine the possibility of bacterial overgrowth in the small intestine, a doctor will review symptoms, medications, and medical history and then perform a physical exam along with a bacterial culture or breath test. Most likely the latter.

Hydrogen and methane breath tests are the safest form of testing for SIBO. Breath tests avoid the possible side effect of directly obtaining a bacterial culture from the small intestine. Hydrogen and methane are produced by intestinal bacteria. When a person has SIBO, greater than normal levels of hydrogen and methane are measured during a breath test that measures these levels after the ingestion of a substrate of glucose or lactulose.

Treatment of SIBO

We can address the treatment of SIBO by following the 5Rs of functional medicine: remove, replace, repopulate, repair, and rebalance.

1. Remove the Cause of SIBO

Treatment involves the removal of the underlying cause of SIBO. Your doctor will help you discover and correct the cause of your SIBO whether it be low stomach acid, improper diet, intestinal dysmotility, intestinal abnormalities, immune deficiency, or a malfunctioning ileocecal valve. Dietary adjustments and antibiotics will be needed in most cases.

Antibiotics: Antibiotics are used to selectively target and kill off the intestinal bacterial strains causing SIBO.

Herbal Antibacterials: Herbal antibacterials can be helpful in reducing unhealthy intestinal bacteria.3 Some common herbal antibiotics include:

  • Enteric-coated peppermint oil – The enteric coating keeps the peppermint oil from being released in the stomach causing irritation and possibly acid reflux and heartburn by relaxing the LES.
  • Garlic
  • Cinnamon
  • Clove
  • Goldenseal

Dietary Adjustments: Dietary adjustments are needed to overcome SIBO. Sugars and starches should be eliminated from the diet. This includes lactose in dairy which is a form of sugar. Eliminating these will help eliminate the bacteria’s food source. Foods to which the patient may be allergic will need to be determined and eliminated from the diet as well. Reduction in food allergens will improve the body’s immune system and its ability to heal from the bacteria overgrowth.

Intestinal Abnormalities: Intestinal abnormalities will likely require surgical repair.

Low Stomach Acid: Causes for low stomach acid were covered under the heading “What Causes SIBO?” above. Eliminating as many of these as possible will improve acid levels. Replacement of acids will be discussed in the second of the 5 Rs.

Intestinal Dysmotility: Proper intestinal motility needs to be established. Your doctor will help you determine the best course of action for your situation. Drinking more water, eating more fiber, changing exercise habits, or changing medications are just a few avenues to pursue when looking to increase intestinal motility.

Malfunctioning Ileocecal Valve: Just as with motility issues water consumption can help with a malfunctioning ileocecal valve. Supplementation or diet change may be needed to correct the problem. Simply chewing food better may be the solution. Your doctor will have to work with you to help pinpoint the problem in your situation and help provide a proper course of action.

2. Replace Nutrients and More

Digestive enzymes, hydrochloric acid, and bile acids are required for proper digestion and should be supplemented when low. These can be replaced by taking supplements and herbs that stimulate their production.

Vitamins and Minerals: Nutritional supplementation is important to replenish vitamin and mineral deficiencies caused by SIBO. If vitamin B12, calcium, magnesium, chloride, zinc, thiamine, and other vitamins are found deficient, replacements will help improve the health and performance of the intestines as well as increase stomach acid (HCl) levels.

Hydrochloric Acid: Betaine HCl is a supplement used to replace stomach acid.

Digestive Enzymes: Digestive enzymes are proteins that help the breakdown of food. Taking a digestive enzyme supplement is often needed when overcoming SIBO.

Digestive Bitters: Digestive bitters can be taken to stimulate the production of stomach acid (HCl), pancreatic enzymes, and bile from the gallbladder. Digestive bitters blends with antibacterial herbs are also available to help kill off unhealthy bacteria while stimulating the digestive system.

Examples of available digestive bitters:

  • Bitters Compound
  • Digestive Bitters
  • Digestive Grape Bitters
  • Organic Bitters
  • Swedish Bitters

3. Repopulate Good Gut Bacteria

Good gut bacteria should be reestablished for optimal intestinal health and to control the growth of unhealthy bacteria. This is done through the ingestion of probiotics and prebiotics.

Probiotics: Probiotics such as bifidobacteria and lactobacillus species can be taken in supplement form or through ingestion of fermented foods such as sauerkraut, miso, kimchee, kombucha, yogurt, and kefir. However, yogurt and kefir may need to be reintroduced later in the treatment process. The sugar found in dairy (lactose) will feed the unhealthy bacteria.

The probiotic foods you choose should be unpasteurized. Pasteurization kills off the beneficial bacteria.

Prebiotics are non-digestible carbohydrates that feed probiotics. Prebiotics are available as a supplement and many foods such as asparagus, artichokes, beets, carrots, radishes, bananas, oatmeal, barley, flax, wheat, garlic, leeks, onion, legumes, and more.

4. Repair Intestinal Health

Repair of the intestine can be facilitated through the use of mucilage and other nutrients.

Mucilage – SIBO can damage the mucous membrane of the small intestine leading to a leaky gut. Mucilage is a substance in plants that can help protect and restore the integrity of mucosa lining the gastrointestinal tract by coating and building up the mucous membrane. The following forms of mucilage can help repair the small intestine.

Nutrients – SIBO can cause a lack in needed nutrients for healing the intestines. Supplying the body with supplements such as L-glutamine, anti-oxidants, vitamins A, C, and E, zinc, and omega-3 fish oils will facilitate healing.

5. Rebalance – Healthy Lifestyle Choices

Lifestyle choices come into play during the rebalancing phase. Stress reduction, exercise, and sleep can all improve intestinal activity by improving the parasympathetic drive and rebalancing hormones. Positive lifestyle choices should be adopted for the long term.

Gas and slowed digestion caused by SIBO causes acid reflux symptoms that can lead to GERD. SIBO treatment can provide relief from acid reflux symptoms like heartburn and serves as an effective remedy for many seeking GERD treatment.


1) Andrew C. Dukowicz, MD, Brian E. Lacy, PhD, MD, & Gary M. Levine, MD. “Small Intestinal Bacterial Overgrowth: A Comprehensive Review.” National Center for Biotechnology Information, U.S. National Library of Medicine, Gastroenterol Hepatol (NY), February 2007.

2) Jan Bures, Jiri Cyrany, Darina Kohoutova, Miroslav Förstl, Stanislav Rejchrt, Jaroslav Kvetina, Viktor Vorisek, & Marcela Kopacova. “Small intestinal bacterial overgrowth syndrome.” National Center for Biotechnology Information, U.S. National Library of Medicine, World Journal of Gastroenterology, June 28, 2010.

3) Victor Chedid, MD, Sameer Dhalla, MD, John O. Clarke, MD, Bani Chander Roland, MD, Kerry B. Dunbar, MD, Joyce Koh, MD, Edmundo Justino, MD, Eric Tomakin, RN, & Gerard E. Mullin, MD. “Herbal Therapy Is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth.” National Center for Biotechnology Information, U.S. National Library of Medicine, Global Advances in Health and Medicine: SAGE Journals, May 1, 2014.

9 Replies to “SIBO and Heartburn”

  1. Hi Steve,

    Are medical doctors (M.D.s) trained to treat this condition? My doctors only want to prescribe PPIs, the easy way out. What questions should I ask of my doctor? And, what treatments are available for yeast infection? I have read that yeasts (Candida) are resistant to antifungals.

    1. Hello Mark,

      Gastroenterologists are trained to treat SIBO, H. pylori and Candida. May doctors do want to treat with PPIs. Different doctors treat illnesses in different ways. You may have to search out a doctor that prefers to steer clear of PPIs when possible. Some people need to be on PPIs for short or long term. Doctors are key in helping determine this.

      Some questions you may ask:
      What are the symptoms of SIBO, H. pylori, and Candida?
      How do you test for SIBO, H. pylori, and Candida?
      What treatment plan do you recommend?
      What risks are involved with the suggested treatment process?
      How long will treatment process take?
      Is there a diet plan you suggest I adhere to?
      How do I protect my liver from additional risk? (Candida has been shown to cause liver damage.)

      Discussion of treatment plans goes beyond what I can write here in the comments. We have an upcoming article planned about Candida. I’ll make note to email you when it’s posted. Though technical there are many great articles about Candida at the National Center for Biotechnology Information, U.S. National Library of Medicine that you might check out. (

      We wish you the best during your treatment process.

    2. Functional Medicine Doctor is most helpful in treating SIBO, in my experience. I’ve been on PPIs for 8 years. It’s al the medical doctor and gastroenterologist were willing to prescribe.

    1. Hello Rob! There is no specific indicator for switching to the next stage of the 5Rs. Your doctor can help advise you as each stage will differ for each individual. Best!

    1. Please see the last section of the article on Treatment of SIBO. The 5Rs of functional medicine can help guide you through natural home remedies for SIBO.

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