Controlling SIBO 
with the Paleo diet

Do you become more constipated when you increase your fiber intake? 
Do you feel bloated when eating almost any food, especially carbs? 
Is your gluten-free diet not giving you the results 
you hoped for in terms of your digestive health? might have SIBO!

Download the free PDF guide to help you get started on the SIBO diet!

SIBO stands for small intestinal bacterial overgrowth. In plain English, it means there is a chronic bacterial infection in your small intestines. It is totally normal to have bacteria in your small intestines but too much at the wrong place can be a problem.

In SIBO, the bacteria that overgrow are not necessarily bad, but there are just too much of them in a section of the intestines where they shouldn’t be in high numbers. Most of the bacteria in your intestines should actually be in your colon or large intestines, not in your small intestines.

The human body is actually made of 10 times more bacteria than human cells...! But most of the bacteria in your GI tract should be concentrated in your colon, not in your small intestines.

Cell numbers!

Human cells and bacteria cells in your bodyThe (big) numbers

Number of human cells in your body10,000,000,000,00010 trillionNormal number ofbacteria in your body100,000,000,000,000100 trillionNormal concentration of bacteria in yourcolonBetween 10,000,000,000and 100,000,000,000/mL10 to 100 billion/mLNormal concentration of bacteria in yoursmall intestinesLess than 100,000/mL< 100 thousand/mLConcentration ofbacteria in your small intestines with SIBOMore than 100,000/mL> 100 thousand/mL

SIBO in History

SIBO is not a new condition, although the name is. Dr. Haas created first published a diet to manage this problem in 1951 after 25 years of successfully treating patients with digestive problems. His diet, refined by Elaine Gottschall, became the 
SCD or specific carbohydrate diet, as published in her bookBreaking the Vicious Cycle, which was recently further modified by Dr. Natasha Campbell-McBride in her book called the
GAPS diet. (5-6)

What are the symptoms?

The most common symptoms of SIBO are the same ones as IBS(irritable bowel syndrome) and mainly affect your gastrointestinal system (2-4, 7):

  • abdominal distension or bloating;
  • excess gas (flatulence and/or belching);
  • abdominal discomfort, pain or cramping;
  • changes in your bowel movements (diarrhea, constipation or alternating constipation and diarrhea).

In addition to these uncomfortable and life-disrupting GI symptoms, SIBO sufferers also experience at least one of these systemic symptoms (2-4, 7):

  • GERD or acid reflux;
  • nausea;
  • malabsorption and nutrient deficiencies:anemia;B12 deficiency;fat soluble vitamin deficiencies (vitamins A, D, E and K);fatty stools;
  • leaky gut:
  • food intolerances, fructose malabsorption and gluten intolerance;
  • joint pain;
  • headaches or migraines;
  • skin problems (hives, eczema, roseacea);
  • concentration issues (brain fog, fatigue);
  • autoimmune disorders (celiac disease, rheumatoid arthritis, diabetes);
  • inflammatory bowel diseases (Crohn’s disease, ulcerative colitis);
  • IBS (irritable bowel disease);
  • asthma;
  • depression;
  • obesity;
  • Autism...

As you can see, the symptoms are not very specific and can affect almost every organ of your body!

How does SIBO cause digestive problems?

If you have an overgrowth of bacteria in your small intestines, as is the case with SIBO, these bacteria will try to get their hand on every piece of carbohydrates or sugar they can to feed themselves. They literally steal foods and nutrients away from you. When “eating”, the bacteria in your small intestines release a lot of excess gas that causes the bloating, belching, flatulence and pain. The type of gas the bacteria in your gut produces can also affect the functioning of your intestines, causing either constipation or diarrhea.

The mechanism is very similar to what happens with 
fructose malabsorption and FODMAP intolerance, except that it is generalized to most carbohydrates.

SIBO and leaky gut (or increased intestinal permeability)

SIBO is also associated with the leaky gut syndrome, or increased intestinal permeability. The role of your gut is to act as a filter: let the nutrients your body need in while keeping toxic substances out. What happens if your gut is leaky? Toxins and incompletely digested food (in other words, pooh!) gets into your bloodstream. Depending on your individual weakness, a leaky gut can induce symptoms in your joints, brain or skin. Even if you don’t have any digestive symptoms, you could still have a leaky gut, but if you have SIBO, you’re likely to have both GI symptoms and leaky gut symptoms.

How do I know if I have SIBO?

Your small intestines are not an easy place to access and it can be hard to know exactly what is going on in there. Current techniques only allow us to see what is happening in the first 2 feet (60 cm), but what happens in the rest of your small intestines (18 feet or 5.4 m) remains, for the most part, a mystery…

The only current standardized method to diagnose SIBO is through ahydrogen/methane breath test. But even breath tests are not totally reliable because they only identify between 20 and 75% of cases…. (3) This is why your symptoms should also be considered in assessing your situation. If you want to get tested, tests can be ordered by mail in most countries for around

There are currently 2 different breath tests currently approved to diagnose SIBO, using either lactulose or glucose. In either case, you are given a sugary solution (lactulose or glucose) and samples of your breath are then taken at regular intervals, for up to 1.5 to 3 hours depending on the sugar used, to check for the amount of methane and hydrogen produced. It is also important to keep in mind that the breath test using glucose as the test sugar can only diagnose proximal SIBO (or the presence of SIBO in the first part of your intestines), while the lactulose may b a better test to determine the presence of SIBO in both the proximal and distal part of your small intestines. (2-4)

Humans don’t produce these gas, only bacteria do, which means that an excess of these gas in your breath indicates an excess of bacteria in your small intestines. If the gas was produced by the bacteria in your colon, the gas wouldn’t be expelled in your breath, but would rather manifest as flatulence. (2-4)

If your test reveals that the excess of bacteria in your gut mainly produces methane, you are more likely to suffer from constipation, while it is usually the opposite (diarrhea), but not always!, for hydrogen-producers. (2-4)

Food intolerances

Many SIBO sufferers believe they have food intolerances before being diagnosed with SIBO, and they actually do as a result of having a leaky gut caused by the bacterial overgrowth. However, testing for food sensitivities is not really useful since SIBO can make you react to almost anything you eat by compromising the integrity of your gut lining. Your best bet is to be patient and use an elimination diet protocol to heal your gut and rebalance your gut flora to improve your food sensitivities. (Food intolerances and sensitivities are not the same as a true food allergy. You cannot get rid of a food allergy, while food intolerances and sensitivities may be improved.)

Stool testing

Some health care providers recommend stool testing for people with GI issues, but it is important to know that although it might reveal useful information, stool testing does not tell anything about SIBO because it cannot differentiate between the flora of your small vs. large intestines. Moreover, your stool test may be completely normal even if you have SIBO because the bacterial infection does not necessarily come from bad/harmful bacteria.

Candida infection

Many people with GI problems may believe they have a candida or yeast infection. Although candida infection can exist with or without SIBO, it tends to be over-diagnosed while SIBO is under-diagnosed. In other words, it is very likely that many of the people who diagnose themselves with a candida infection actually suffer from SIBO. ­­

Learn more about the book "Digestive Health with REAL Food" →

How does SIBO develop?

Why would you have a bacterial overgrowth in your small intestines? Healthy people have normal mechanism barriers to control the number of bacteria in your gut, but if one of these mechanisms doesn’t work properly, they could make their way in your small intestines and multiply to the degree of becoming a chronic infection (SIBO). Here are a few possibilities:

  • Low stomach acid­­­

Enough stomach acid is essential for a healthy digestion. Not only does stomach acid helps you break down food, activate digestive enzymes and enhance nutrient absorption, it is also important to kill bacteria and prevent infections. If your stomach acid levels are low, which can be as a result of stomach acid-lowering medications,stress or even years of following a vegetarian diet, bacteria can more easily make their way into your small intestines where they can overgrow and cause SIBO.

  • Impaired migrating motor complex

The intestines are not only a simple tube through which food passes; they have many important functions. One of them is to contract, as a muscle would, to clean your intestines. This special movement made at regular intervals throughout the day is called the migrating motor complex (MMC) or cleansing waves. Think of it as your small intestines sweeping themselves to remove debris and keep bacteria from staying where they should not. The MMC can be impaired bystress or by eating too often (constant snacking). On the other hand, you can promote MMC by using relaxation techniques and keeping your meals at least 4-5 hours apart.

  • Gastroenteritis

Suffering from an infection in your gastrointestinal tract, either caused by bacteria or parasites, can alter your gut flora. Infectious bacteria and micro-organisms can secrete toxins that inactivate the MMC, one of the important mechanism required to prevent SIBO. In addition, gastroenteritis is often treated with antibiotics, which can further compromise your gut flora and lead to SIBO.

  • Medications

 and the birth control pill are some of the medications that can severely impair your gut flora. If you have been on any of these, or both, at some point in your life, you are more likely to havegut dysbiosis (an imbalance in your gut flora) and are therefore more at risk for developing SIBO.

  • Stress
Stress inhibits with two of the most important mechanisms to protect us against SIBO: it lowers proper stomach acid secretionand interferes with the MMC, the intestines’ cleansing waves. Relaxation techniques and learning how to have more positive thoughts can make a big difference for both your mental AND digestive health.
  • Standard American diet
A poor diet rich in carbohydrates, refined flours and sugars can be the perfect ground for developing SIBO since bacteria love carbs!Constant snacking inhibits regular MMC to keep bacteria in controlled numbers within your small intestines.
  • Combination of factors!
For many people, a combination of many of the above factors is what ultimately results in the development of SIBO.

What are the treatment options?

  • Antibiotics
Your doctor or your naturopathic doctor can prescribe eitherantibiotics (i.e. Rifaximin) or herbal antibiotics. Studies have shown that they are very effective at getting rid of SIBO... for a few weeks. Recurrence rates are unfortunately very high, especially if proper dietary changes are not made. Rifaximin, the most studied antibiotic for SIBO treatment, is very expensive. A treatment can easily cost over $1000-2000 and is usually not covered by health insurances. (3-4)
  • Elemental diet
An elemental diet is a like a pre-digested formula that contains pre-digested carbohydrate (glucose) and pre-digested protein (amino acid) as well as some fat. If you choose this approach, you would need to replace all of your meals with the formula for at least 2 to 3 weeks. The goal is to starve the bacteria. Although studies show that this method can be very effective at eradicating SIBO, the benefit is usually only temporary if dietary changes are not made. Elemental diets taste awful and can also be very expensive, costing at least $900-1350 per treatment (rarely covered). (3-4)
  • Diet only
Although this approach can takes months, if not years, it is likely to be the most successful in the long-term. The goal is to starve the bacteria causing your SIBO. Eliminating most carbohydrates, especially polysaccharides (starches) and most sugars (especially in the form of disaccharides) is the approach recommended by the SCD and GAPS diet. (5-6) Dr. Siebecker believes that this approach can take 2-3 years on average and that is should be followed strictly for 1 year past no symptoms before liberalizing the diet. (3) [Learn more about Dr. Siebecker and her work at or take her online webinar.]

I believe that combining this low-carb diet (which allows carbs from tolerated non-starchy vegetables and monosaccharides) with the low-FODMAP diet (FODMAPs = short-chain fermentable carbohydrates or fructose, oligo-, di-, mono-saccharides and polyols) and the Paleo diet(grain-free, legume-free and processed food-free), while including gut-healing element, is the best approach for SIBO.  

Download the free PDF guide to help you get started on the SIBO diet!

Even if it takes time to completely restore your gut flora and completely heal your gut, most people can see drastic improvements in their symptoms within the first weeks.

Whatever treatment option you choose, you should alwaysCOMBINE it with a proper diet (ideally low in carbs to prevent recurrence and low in gut irritants to allow your intestines to heal) as well as stress management/relaxation techniques. Working with a health professional familiar with SIBO is recommended for best results.

What foods should you avoid?

Avoid foods containing nutrients that can be fermented by the bacteria in your small intestines before you have a chance to absorb them as well as gut irritants:

  • Most carbohydrates and fibers that can feed bacteria/SIBO: starches, sugars, prebiotics, FODMAPs and soluble fibers.
  • Gluten because of its role with zonulin and intestinal permeability (leaky gut).
  • Gut irritants: grains, legumes, soy, caffeine, nuts, nut flour, dairy, nightshades, alcohol, MSG, artificial sweeteners, processed ingredients, NSAIDS, BCP...
  • Pro-inflammatory foods: vegetable oils high in omega-6 fats, grains, processed foods and any food you are intolerant to.

What foods should you eat?

  • Healthy fats: coconut oil, ghee, EVOO, macadamia oil, avocado oil, homemade mayonnaise made from healthy oils, animal fat from pastured animals.
  • Protein: meat, fish, poultry and seafood, ideally from pastured animals; eggs if tolerated.
  • Plant food: low-carb, non-starchy and low-FODMAP vegetables; high-FODMAP vegetables, fruits and nuts if tolerated.

Other important tips for SIBO

  • Chew your food well to make sure you absorb your food before the bacteria do;
  • Space your meals every 4 to 5 hours and try to fast overnight (for at least 12 hours) to help with the MMC;
  • Relax and avoid stress as much as possible to promote adequate stomach acid and normal MMC;
  • Keep a food journal, introduce foods one a time every 3-4 days and assess your individual tolerance;
  • At first, make your food as easy to digest as possible: make stews, cook your vegetables thoroughly (peel and deseed them if necessary too) and even puree your vegetables;
  • Include homemade bone broth in your daily routine to promote gut healing;
  • Slowly introduce probiotics (from supplements or fermented foods) to re-balance your gut flora;
  • Be aware that die-off symptoms (a worsening of your previous symptoms or new symptoms) is common during the first weeks... stick to your diet and things will get better;
  • Talk to your doctor before changing any medications/supplements or consult the Paleo dietitian for help controlling your SIBO.

Download the free PDF guide to help you get started on the SIBO diet!

Learn more about the book "Digestive Health with REAL Food" →

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References (1) Kopacova M. Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology. 2010; 16(24): 2978-2990. (2) Siebecker A. About SIBO. [accessed online:](3) Siebecker A. Small Intestine Bacterial Overgrowth: Clinical Strategies. 2011. [recorded webinar:] (4) Pimentel M. A New IBS Solution. 2005. (5) Gottschall E. Breaking the Vicious Cycle: Intestinal Health Through Diet. 2004. (6) Campbell-McBride N. Gut and Psychology Syndrome: Natural Treatment for Autism, Dyspraxia, A.D.D., Dyslexia, A.D.H.D., Depression, Schizophrenia. 2010. (7) DiBaise JK. Nutritional Consequences of Small Intestinal Bacterial Overgrowth. Practical Gastroenterology. 2008: 69: 15-28. (8) Gasbarrini A, et al.Small Intestinal Bacterial Overgrowth: Diagnosis and Treatment. Digestive Diseases. 2007; 25: 237-240. (9) Giamarellos-Bourboulis EJ and Tzivras M. Small Intestinal Bacterial Overgrowth: Novel Insights in the Pathogenesis and Treatment of Irritable Bowel Syndrome. Annals of Gastroenterology. 2009; 22(2): 77-81. (10) Olendzki B, et al. Pilot Testing a Novel Treatment for Inflammatory Bowel Disease. University of Massachusetts (UMass) Medical School and UMass Memorial Health Care. 2011

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