Modifying Paleo for Small Intestinal Bacterial Overgrowth

July 3, 2012 in Categories: , , by

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Small Intestinal Bacterial Overgrowth (or SIBO) is a chronic bacterial (and/or yeast) infection of the small intestine, characterized by excessive number and/or abnormal type of bacteria (and yeast) growing in a part of the gastrointestinal tract that normal contains relatively few microorganisms.  These bacteria can cause a variety of problems by interfering with digestion and absorption of nutrients and by damaging the lining of the gut, causing a “leaky gut” (I addressed the many health problems that can arise from a leaky gut in this post). 

The most common symptoms of bacterial overgrowth include abdominal pain, nausea, bloating, gas, belching, flatulence, chronic diarrhea, and chronic constipation.  These symptoms are due to the large volume of bacteria the digestive tract (alive and dead, as they read the end of their lifecycle) and the large amount of gas and metabolic waste that they produce.  Many more symptoms of SIBO are a direct effect of nutrient malabsorption.  This arises either from the bacteria metabolizing those nutrients before we can absorb them or by the bacteria causing enough inflammation in the lining of the gut that it the gut can’t work properly anymore.   For example, the bacteria preferentially consume iron and vitamin B12, causing anemia.  The bacteria decrease fat absorption by deconjugating bile leading to deficiencies of vitamins A & D and causing steatorrhea (fatty stools).  As the gut lining becomes increasingly inflamed and leaky, larger and not fully digested food particles enter the body, causing an immune reaction which leads to food allergies and food sensitivities.  Bacteria themselves can enter the blood stream causing systemic inflammation and immune reactions that can lead to autoantibody formation and autoimmune diseases (for a comprehensive review article see the footnote). 

SIBO was only described in the late 1990s and is still grossly underdiagnosed. This is partly because many patients don’t seek medical attention for their SIBO symptoms, because many doctors aren’t aware of its prevalence and don’t consider it in their differential diagnostics, and because the tests for SIBO still have fairly high false negative rates (where you have the disease but the test says you don’t).  As SIBO becomes more recognized, it is also becoming inextricably linked with many other diseases.  Many physicians and scientists now believe that Irritable Bowel Syndrome (the cause of which has never been properly defined) is actually a group of symptoms caused by SIBO (see the book The New IBS Solution).  SIBO is also often associated with Crohn’s disease, Celiac disease, short bowel disease, various liver diseases, fibromyalgia, some autoimmune diseases (such as scleroderma, diabetes, lymphoma, and chronic lymphocytic leukemia and the aforementioned Crohn’s disease and Celiac Disease) and even rosacea (for a fantastic summary of confirmed related diseases, see  Whether SIBO is a causal factor or a symptom of these diseases remains to be determined.  Given how new all of this science is (and how prevalent SIBO actually is!), I suspect that over the next few years many more health conditions will linked with SIBO.

How do you know if you have SIBO?  If you have digestive symptoms, especially if they persist after adopting a strict paleo diet, SIBO is a possibility.  You can opt to get tested (there are several different test options which can be ordered by your primary care physician), however know that the current testing methods are not 100% reliable.  One of the easiest ways to determine whether you have SIBO is to see if diet modifications aimed at treating it make you feel better. 

How can you fix SIBO?  There are two diets (very similar to each other) that have been developed with the intention of starving the bacteria in the small intestine and healing the damaged lining of the gut.  These are the GAPS (Gut and Psychology Syndrome) diet(see Gut and Psychology Syndrome) and the SCD (SpecificCarbohydrate Diet) diet (see Breaking the Vicious Cycle).  The general approach to these diets is to eliminate any dietary sugars that are not monosaccharides.  Monosaccharides are simple sugars like glucose and fructose and are the most easily absorbed in the digestive tract.  More complex sugar molecules like sucrose (i.e., table sugar which is a disaccharide) and starches have to be broken down into monosaccharides before they can be absorbed.  This means that the sugar takes longer to be digested, which means it travels farther down the digestive tract before being completely absorbed, which means that some of it reaches the abnormal bacteria growing in the small intestine and provides a food source for them.  These diets also focus on consuming healing foods such as bone broth, conjugated linoleic acid found in the fats from grass-fed animals, and coconut oil.  I recommend combining one of these diets with a paleo diet for the most rapid and effective reversal of SIBO.

A standard paleo diet is typically not enough to treat and reverse SIBO.  Attention also needs to be paid to the amount and types of carbohydrates being consumed.  I recommend following a paleo diet with modifications disallowing starchy vegetables and high sugar foods as per the SCD and GAPS diets (see my post Fruits and Starchy Vegetables with SmallIntestinal Bacterial Overgrowth).  Many people may find taking Apple Cider Vinegar before meals (as outlined in TheStomach Acid Connection) is helpful.  For more severe cases digestive supplements may be beneficial (I am not familiar enough with these to recommend a particular brand, type or dose.  Recommendations can be found in The Paleo Solution, It Starts With Food, and this post from Chris Kresser.  If you need personalized recommendations, I suggest contacting Diane Sanfilippo at  You may also find some good information in my posts Repairing the Gut and What Should You Eat to Heal a Leaky Gut?  I also want to mention that stress management is very important (see my post How Mood and Gut Health Are Linked).  Homemade bone broth and a source of Vitamin D(sunshine, liver, supplement) are particularly important to promote healing.  A source of diverse probiotics (from fermented foods like Sauerkraut,coconut milk kefir, or Kombucha and/or from a high quality supplement) help to restore normal gut microflora (it’s better to keep the dose of these beneficial bacteria on the low side, at least at first, since they can add to the high volume of bacteria and increase symptoms if you’re too aggressive).  In extreme cases, a doctor may recommend a course of potent antibiotics followed by a gut-healing protocol (exactly what is outlined above) and probiotics.  For those with symptoms indicating the early phases of autoimmune conditions (see my post You May Have an Autoimmune Disease But Don’t Know It), following the Autoimmune Protocol for the first 1-3 months may be very beneficial.

Correcting SIBO can take up to 2 years.  However, you should see improvement in your symptoms fairly quickly with gradual and continuous improvement (if you don’t, it’s worthwhile considering a FODMAP sensitivity as a confounding factor, which I will be discussing in my an upcoming post).  Stress, poor sleep, infections and poor diet choices can all create setbacks.  It is always difficult to commit to more restrictive forms of a paleo diet (which can be tough enough as it is!).  I have what I believe is a mild case of SIBO.  Because I follow the Autoimmune Protocol, I rarely have issues now.  However if I slip and eat a high carbohydrate food, I fairly rapidly suffer intense bloating followed by days of gas pains and constipation.  It’s not fun to follow such a restrictive diet, but is it worth it!

Bures J. et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010 June 28; 16(24): 2978–2990.


i have a j-pouch and struggling bad for several months. Butternut squash/zuchinin squash/carrot-sweet potato are my daily diets. I ma wondering if this may be aggrevating my symtoms and inflamations?

It definitely could be, I just took all starches out of my diet (so sweet potatoes and butternut squash) and my bloating in my stomach as well as other symptoms quickly diminished

My OBGYN says I have IBS, and has diagnosed me with endometriosis. She removed my left fallopian tube and ovary to help me with the pain I was having in my abdomen on the left. But now the pain has returned. It it possible that this is SIBO and not IBS?

Hi! I don’t have many of the symptoms of SIBO, but I have had blood tests showing I am deficient in various vitamins like Vit D and B12, plus my serum Ferritin levels are low. I have to take pretty heavy supplements to keep those levels up. I have been wondering why I am so deficient when I eat a healthy Paleo diet. Could I possible have SIBO even without the gas, bloating, cramps, etc? I followed the AIP diet this spring and felt good, but didn’t notice anything major when I reintroduced eggs, nightshades and dairy. I am planning on trying it again and being even more careful with my reintroductions (waiting 2 weeks in between, for example) but perhaps I should consider starting with the GAPS or other SIBO diet instead? Thanks for your insight.

It sounds like I may have SIBO. However, I have been following a paleo and low-GI diet because I have Candida and food intolerances. If I add the SIBO restrictions to that, it doesn’t leave me with much to eat! I’m starting to wonder what is good for me to eat…

I do have SIBO (the constipation variety) and have twice taken the antibiotic for it. I just finished my second dose of Rifaximin. My doctor currently has me on the low FODMAP diet which I have been on for one month. I am not sure this diet is correct for me as grains are a huge issue for me. I ate quinoa and was ill for three days after I ate it. Sweet potatoes and regular potatoes cause suffering as well. I cannot eat gluten, and that was established well before the SIBO entered the picture. My doctor tested me for celiac, but since I had not eaten it for a while, it did not show up. I don’t know if I should continue on the low FODMAP diet to see if that helps, minus the grains or switch to the specific carb diet. Any ideas would be greatly appreciated. I cannot wobble even a little on my eating or I will suffer dearly for days. :(

Sarah has consultants available at that can help troubleshoot diet/health issues. She also recommends and – Christina, Sarah’s assistant

[…] My Health Journey has been no different and last week I discovered that I have SIBO – Small Intestinal Bacterial Overgrowth which refers to a condition in which abnormally large numbers of bacteria are present in the small intestine: the types of bacteria found in the small intestine are more like the bacteria found in the colon and they don’t belong there (To read the The Paleo Mom’s Overview of SIBO can be found here) […]

Thanks for the post. I always wanted to do a month of paleo because I suspect a chronic bacterial overgrowth. But it is extremely tough to make it past 7 days. The body seems to be starved and I am losing weight too fast.
But I think I will try one more time…

I have had SIBO for many years, and after experiences only a minute improvement with the diet, I tried the medication. My test results showed some improvement, but when I was retested a few months later it was worse that ever. My doctor said she had never seen a case so bad, and didn’t have any suggestions. Have you ever heard of this occurring with anyone else, and have any suggestions?
Any advice would be much appreciated!

Hi I just read your article and you give lots of advice as to what you in particular suggest. Are you a natropath or a doctor? Just wondering if it is a personal opinion or a medical one. Thanks

I am a bit confused. Are you saying you recommend combining Autoimmune Paleo with GAPS or SCD or low FODMAP or some combination? Or just doing Autoimmune Paleo on it’s own being enough? It seems like doing a combination of those would severely limit allowable foods, and just one of these diets alone is restrictive already, so I want to make sure I understand correctly. I definitely have autoimmune problems and leaky gut and SIBO doesnt seem too far fetched, but Paleo seems to really cause me severe mood instability (I am suicidal in only a few days after starting strict Paleo, no matter how many carbs I eat from squashes and dates etc.) and I don’t know why, and so I am obviously not thrilled with limiting more than is necessary while struggling that much emotionally, no matter how great it makes my guts feel.

Sarah or one of Sarah’s assistants might want to update this article. This post was from 2012 and it looks like more research has been done on this topic (since this is of course a new area of research that seems to be growing rapidly). I just got done watching an interview with Chris Kresser and Steve Wright discussing this exact topic. Chris Kresser has very different things to say about this subject matter, even though it was also about yeast (but he states that this usually goes hand-in-hand with other overgrowths or infections). I found the link on Mickey Trescott’s site.

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