SIBO and FODMAPs – What They Mean and How They Affect Your Health.

Originally published May 21, 2015 on

SIBO has gotten a lot of press recently, most likely due to its increasing prevalence in recent years. SIBO stands for small intestinal bacterial overgrowth, and is defined as a chronic infection of the small intestine. The most common symptoms of SIBO are very similar to that of IBS - namely gas, bloating, diarrhea, constipation, leaky gut, fructose malabsorption and excessive fermentation of certain carbohydrates called FODMAPs. If you’re suffering from SIBO you may also experience eczema, joint pain, headaches, asthma, depression, autoimmune disorders and a multitude of food sensitivities. According to research by Dr. Mark Pimental, 84% of people with IBS have bacterial overgrowth in their small intestine which could suggest that most people who complain of IBS symptoms also have SIBO. (Most IBS patients are FODMAP intolerant, but while consuming FODMAPs exacerbates symptoms, it doesn’t actually cause IBS.)

But wait a minute, isn’t bacteria in our gut a good thing? Yes! But only if it’s in the right place. Our bodies have about 10 times the number of bacteria as we do human cells, but the large majority of those bacteria should make their home in the colon. When too many bacteria set up shop in our small intestines they rob us of nutrients such as B12 and iron. These bacteria also deconjugate bile acids produced by the liver which prevents proper fat digestion and absorption creating problems similar to not having a gallbladder. Not only do we miss out on the benefits of fats themselves, but we also cannot absorb fat-soluble nutrients such as Omega-3 fatty acids, CoQ10, beta-carotene and vitamins A, D, E and K.  So if you’re supplementing with these and not seeing the expected improvement, SIBO could be a potential culprit. Your doctor can administer a simple breath test or an organic acid urine test to determine if you have SIBO.

SIBO can also contribute to both weight loss due to malnutrition and obesity. If the excess bacteria are consuming all the carbohydrates in your diet, you may lose too much weight accompanied by nausea, vomiting and lack of appetite. Chronic diarrhea also deprives you of the nutrients in your food because it’s moving through your body too quickly to be absorbed. Insulin resistance and elevated cortisol levels can also be a product of the stress and inflammation from SIBO, resulting in weight gain, weight loss resistance and possible contributing to diabetes.

SIBO is often caused by dysbiosis – or an imbalance between beneficial bacteria and yeasts and harmful bacteria, yeast, and even parasites, but our diet may be the biggest cause. Bacteria thrive on the sugars and starches in the food we eat and the byproduct of this is fermentation. Aglaée Jacob, author of Digestive Health with Real Food describes the bacteria as creating “lots of microbreweries”. So just like the process of brewing beer, the more food we provide for the bacteria, the more fermentation they produce, which translates to gas and bloating. In turn that gas and bloating cause inflammation in the gut, eventually leading to the symptoms mentioned above.

Dietary Interventions for SIBO.

The trick when it comes to getting SIBO under control is similar to that of treating a candida infection – starve the bacteria without starving the person. In this case that means removing their favorite foods – sugar, starches and fermentable carbohydrates. Enter FODMAPs. FODMAPs stands for fermentable oligosaccharides, disaccharides, monosaccharides and polyols and following a low FODMAP diet has proven to be extremely effective in the treatment of IBS and SIBO.

FODMAPs are all types of carbohydrates that are not fully digested and absorbed by the GI tract and are therefore more easily fermented by the bacteria who thrive on them. As a general rule of thumb, good bacteria thrive on properly digested food while undesirable bacteria thrive on undigested foods such as FODMAPs. Proper digestion of food by stomach acid, pancreatic enzymes and enzymes found in the intestinal “brush border” breaks food down into particles small enough to be absorbed by the body. If this process doesn’t work efficiently, bacteria can easily overpopulate in the small intestine and wreak havoc on our health.

When it comes to SIBO, the importance of reducing gut inflammation, adequate stomach acid and enzyme activity cannot be overstated. Healthy intestinal cells secrete immune system antibodies, or immunoglobulins, which act as natural antibiotics to kill harmful bacteria and prevent them from colonizing the intestinal wall. If someone lacks sufficient Vit. D, the secretion of these immunoglobulins is inhibited. Combine this with insufficient stomach acid, enzymes, bile secretions, and constipation and you have the perfect environment for bacterial overgrowth. You can read more about how to increase your digestive ability in this article

Other important factors here are hydration and the migrating motor complex or “cleansing wave” of the intestines. This process kicks in a few hours after a meal and acts like a push broom, sweeping undigested food and bacteria from the stomach, through your small intestines into the colon. These waves only occur when the body is not digesting, so eating more often will inhibit this process and promote growth of bacteria in the small intestine. Adding insult to injury, these bacteria then produce toxic secretions that can cause long-term damage to your intestines and migrating motor complex if left untreated. 

Drinking enough water throughout the day is essential for proper bowel motility and preventing constipation. You can increase and preserve your cleansing waves by staying hydrated and eating 3 meals a day, 4-5 hours apart. However, do not wait this long between meals if you have blood sugar regulation issues, are malnourished and/or underweight.

What to eat and what to avoid on a low FODMAP diet.

People with SIBO often develop intolerances to a multitude of non-FODMAP carbohydrates, and can benefit significantly from a low-starch, gluten-free, paleo type diet rich in low FODMAP vegetables, healthy fats and clean, organic protein sources. Happily this type of diet can also inhibit the growth of other pathogenic intruders such as candida and parasites.

Since legumes are one of the biggest offenders when it comes to fermentable carbohydrates, vegetarians who rely on them as a protein source will want to substitute plant-based proteins such as hemp protein powder, hemp hearts, pumpkin seed protein, spirulina and kale.

It is important to point out that while higher FODMAP foods may be problematic for those with SIBO, it does not mean that they are unhealthy. There are many wonderful and highly beneficial foods, especially vegetables that should be reincorporated into the diet once SIBO is resolved. If you do not suffer from IBS or SIBO there is no reason for you to avoid high FODMAP nutrient powerhouses such as broccoli and cauliflower unless you have specific intolerances.

On average it takes about 2 years and sometimes as long as five for SIBO to be completely corrected and for this reason many people choose to treat SIBO with a combination of diet and other treatments. Additional treatment options include antibiotics (usually refaximin and/or neomycin), herbal antibiotics (e.g. peppermint oil, grapefruit seed extract, berberine, etc.) and elemental diets (often very expensive and impractical). Talk with your doctor to determine the best option for you.

While using diet alone to treat SIBO can take much more time and effort than other treatments, some people may start to feel improvement within a few weeks. The overgrowth itself will take longer to resolve, but in the meantime people can enjoy some relief from their symptoms. Dietary treatments for SIBO should only be followed for an additional two weeks after being symptom-free, depending on the severity of the infection. It is not intended to be a permanent protocol and it can be detrimental to your healthy gut flora if followed for too long. 

The goal with this diet is to reduce fermentation, inflammation and undesirable bacteria in the gut. Once those components are under control we can begin healing the gut with specific treatments and begin adding certain foods back in to promote a healthy population of beneficial flora. 

Most Common High FODMAP Foods (see resources below for complete lists):

Vegetables: Artichoke, asparagus, bean sprouts, broccoli, Brussels sprouts, cauliflower, celery, garlic, sugar snap peas, onion, Jerusalem artichokes, potato (all colors), seaweeds, sweet potato, turnip.
Fruits: Apple, apricot, avocado, blackberry, canned fruit, cherries, cranberry, dates, grapefruit, mango, nectarine, papaya, peach, pear, persimmon, plantain, plum, prunes, watermelon.
Grains: Wheat and all gluten-containing grains, amaranth, barley, buckwheat, corn, millet, oats, quinoa, rice, rye, spelt, teff, wild rice.
Legumes: Cannellini beans, chickpeas/garbanzos, fava beans, kidney beans, navy/white beans, pinto beans, soy beans, peas, pretty much all of them.
Dairy products: All dairy products except butter, cheese aged 1+ months, dry curd cottage cheese, ghee, sour cream (homemade), yogurt (homemade).
Proteins/Meats: Bacon w/sugar or corn syrup, broth made with onion or garlic, deli/processed meats.
Nuts/Seeds: Cashews, chia seed, flaxseed, hazelnuts, pistachios.
Fats: Margarine, soybean oil.
Sweeteners: Honey (sage or tupelo), maple syrup, molasses, sugar alcohols (xylitol, erythritol), stevia with inulin or other caking agent, sucralose, sugar/sucrose.
Beverages: Almond or other nut milk w/thickeners, coffee substitutes, coconut milk w/thickeners, fruit juice, soda, chicory tea, licorice tea, pau d’arco tea, soy milk.
Seasonings/Condiments: Asafoetida powder, balsamic vinegar, carob, chicory root, cocoa, all gums/thickeners, spices with onion & garlic, soy sauce/tamari.
Alcohol: Beer, brandy, hard cider, liquors/cordials, rum, sake, sherry, tequila, wine (sweet/dessert), port, sparkling wine.

Additional tips for managing or preventing SIBO:

•    Eliminate foods you are sensitive or allergic to.
•    Omit grains, dairy and higher FODMAP foods.
•    Take digestive enzymes and/or HCl or other digestive support.
•    Eat 3 meals daily with 4-5 hours between each unless you are underweight or  hypoglycemic.
•    Supplement with Vitamin D if you are deficient.
•    Manage stress.

The list of foods to enjoy and foods to avoid is too long to list in detail here, but there are many great resources for low FODMAP diets, including Dr. Allison Siebecker’s web site and these helpful charts from Aglaée Jacob and The Whole 30. There are also two great smartphone apps which you can use to look up specific foods - The Monash University Low FODMAP Diet App and the SIBO app by Dharmaworks Consulting, LLC. I find these especially handy when I’m at the grocery store or a restaurant and need to see if a food is high in FODMAPs.


Aglaée Jacob, M.S., R.D., Digestive Health with Real Food (Paleo Media Group, LLC, 2013)

The Elimination Diet: Discover the Foods That Are Making You Sick and Tired--and Feel Better Fast, by Tom Malterre and Alissa Segersten (Grand Central Life & Style ©2015)

A New IBS Solution: Bacteria-The Missing Link in Treating Irritable Bowel, by Mark Pimentel (Health Point Press ©2006)  

Low-FODMAP diets: are they safe in the long-term? By Aglée Jacob, MS, RD, Feb. 16, 2015 Radicata Medicine

FODMAPs: Could common foods be harming your digestive health?, by Chris Kresser, JULY 13, 2012

Review article: fructose malabsorption and the bigger picture, P. R. GIBSON, E. NEWNHAM, J. S. BARRETT, S. J. SHEPHERD andJ. G. MUIR, Article first published online: 3 NOV 2006

FODMAPs Diet by Dr. Stephen Gangemi, DC

*All articles and information on this website are for educational purposes only. This information is not intended to diagnose, cure, treat or prevent any disease and is not to be regarded or relied upon as medical advice. These statements have not been evaluated by the Food and Drug Administration. Results may vary per person. Discuss any dietary changes or potential dietary supplement use with your health practitioner and do not discontinue any prescription medications without first consulting your doctor.