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.

Coming in late on this but in case anyone has a similar question:

You shouldn’t be losing that much iron even though you’re female. (The actual amount of blood lost in a normal period is maybe 2 to 7 teaspoons. It looks like more because you’re shedding uterine lining too, which has blood vessels all through it.) It’s actually pretty normal to *increase* ferritin as we age. So if yours is constantly low, you’ve got a slow bleed somewhere. If your doc hasn’t checked you for blood in your stool, ask about it. My brain is going to “inflammatory bowel disease or stomach ulcer” just because I’ve been reading about IBD tonight and if you’ve got an ulcer somewhere along your GI tract, that could be enough to cause the problem. Actually, while you’re at it, consider shopping for a new doctor, too.

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 doctor diagnosed with IBS and sent me home with a piece of paper she wrote “FODMAP” on. After years of struggling and attempting different options I was frustrated with no results with little support from my GP and it continued to get worse. Finally I decided to see a naturopath that came recommended to me. It’s been an amazing experience and am beginning to see relief. She’s worked with me and even asked me questions my doctor never bothered to asked. I was shocked and bewildered by the depth in her assessment process. The test for SIBO isn’t even available in Canada and had to be ordered from the U.S. my results came back off the charts. It’s a long process and am continuing to work through it. It’s a complete lifestyle change until it become rectified and reversed. But to now begin to see improvements in my energy, anxiety and mood levels, to now feel some relief in my bloating and constipation, it makes the process so much easier and well worth it. You can find a SIBO specific diet online. it looks much like the FODMAP but does vary and I’ve had to cut ALL grains out of my diet. But the results have been night and day. Hope this helps.

For me, when I have a SIBO/iBS flare up, I cut right back on vegetables (they are very nutritious, but only when absorbed), and cut out fruit and nuts. I stick to a meat/fat diet with lots of bone broth and coconut kefir. This helps tremendously. I will have coconut kefir in the morning (probiotics on an empty stomach) then take my supplements. When I am hungry I will have a piece of salmon or some eggs cooked in coconut butter with a cup of broth, and for dinner (I usually eat 2-3 times per day without carbs causing insulin spikes) slow cooked meat in broth with a good dollop of coconut butter or ghee.

Constipation sibobis typically methane sibo which requires neomycin as well as xifaxan together. I was given only xifaxan & had no results. I did my research & realized what went wrong.

Foods high in fermentation potential? That would be carbs. When was the last time you saw someone make beer with butter or steak? You can preserve those things with an already ongoing fermentation process, but you can’t really ferment *them*.

Actually it really annoys me the way writers of various diet books will turn around and backstab authors of similar books and approaches even though, if you take a good hard look at their prescribed methodology, it isn’t all that different. Kind of like the Paleo community taking potshots at Dr. Atkins even though you can adapt Paleo to an Atkins template. People need to be more honest about this stuff because our end goal should be to help people, not to pit them against one another in dietary one-upmanship.

(My favorite example of this was the media fawning all over Dr. Agatson, the creator of the South Beach Diet, because he’s a cardiologist. Funny, Dr. Atkins was one too.)

[…] 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!

Jessica- yes, I have heard of this. A close friend of mine (I call her my autoimmune sister as we are both battling thyroid issues and have been on the same health journey)…has chronic SIBO and was told the same thing. She did 3 rounds of the antibiotic and she was worse. The integrative Dr. she sees suggested treating it with an anti-fungal (SIBO and candida have a close connection). A few rounds of anti-fungal helped her immensely. May want to look into that. Hope it helps.

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.

Thank you for the comment and the link. In all that I understand there is a close connection between SIBO and Candida.


I really need some help! I am a 19 year old individual with Ulcerative Colitis and SIBO so I am a little confused as to which diet I should follow the Sibo or the Autoimmune Paleo diet. Because doing both at the same time restricts so much food I end up losing weight. I also have some adrenal issues (fairly low cortisol). Any suggestions?

I am unable to eat anything fermented or I spend at least a week suffering and losing weight. I had some miso soup a couple days in a row and now I’m flattened. I’ve had SIBO for at least 10 years now after a severe food poisoning incident. On a paleo diet, but lost way to much weight so added some jasmine rice to it and have gained a few lbs. It seems to agree with me fortunately. I’ve done a course of the antibiotics and for a couple of weeks was OK, but it came roaring back! Does anyone have any experience with going on the starvation liquid diet to starve them out? I don’t know if I can do that as I’m so underweight. But this is killing me.


Edy, I’m with you. I’ve lost way too much weight just eating green veggies and meats. I know I have sibo and refaximin has helped before but I don’t know where to turn. Starvation liquid diet? I already think I’m starving to death because I keep losing weight no matter what I eat.

I am in your camp. I did AIP for 3 months and while it helped a LITTLE, the real thing that improved me was rifaximin – twice. Ultimately my major GI symptoms got far worse on AIP. The bone broth made me very ill. I tried to just push through the bone broth but after weeks it was giving me so much acid and nausea I couldn’t see any benefit. I tried HCL which made my acid explode for days. I’m shocked this works for anyone as it made me physically ill. I really hoped this diet could help me. All it did was starve me – it is tough for me to digest vegetables and thus….. At this point, I eat a varied diet and take enzymes and probiotics and practice biofeedback breathing and meditation. I have days with no symptoms and then days with a lot of symptoms so I breathe and eat rice and pretzels which calm my stomach. It’s a drag but on AIP, SCD, Jamie Koufman’s low acid diet, Norm Robillard’s diet and FODMAPs, I had acid and gastritis symptoms all day every day. I credit the rifaximin for the improvement I’ve seen and perhaps the probioitics and definitely magnesium supplements I take each day. The problem with now is I am eating too much but it does keep my stomach settled. I am once again overweight (lost 20 lbs in 3 months on AIP, gained it back off AIP) and feel like only if I have something in my stomach all the time (eat every 2-3 hours – also the starvation/letting your stomach empty aspect of AIP made me very ill) can I keep my symptoms (upper GI distress, gastritis, acid reflux, excema, asthma) under control. My doctor was open to AIP but told me to stop after 3 months because he felt if I didn’t feel any improvement by then, it was the wrong diet for me. All of these bone broth, meat heavy diets make my gastritis symptoms horribly worse. That said, my joint inflammation was improved, my skin was much better but my stomach was just terrible. At this point, I’m eating a varied diet (but not too many fruits or veggies) taking digestive enzymes and soil probiotics. For me, after months of experimentation, this is the closest I get to relatively normal although the foods that work best for me are all forbidden in AIP (small amounts of nuts, small amounts of pretzels or crackers, beans, rice). But my skin is not so great anymore which tells me that it helped SOMETHING but my stomach couldn’t take it.

Other diets tried: 6 months on FODMAPs, again tiny improvement but really nothing miraculous in any way. Norm Robillard’s diet – too much acid!. SCD – since I have trouble eating veggies, I was very hungry which gave me a ton of acid. Then I did SCD with rice (which I know breaks every rule) which actually worked pretty well – my acid went away – but I was so hungry it was pretty goofy.

Interesting! I have been diagnosed with SIBO. When I have bad symptoms, the thing that helps the most is to eat pretzels – and having my stomach empty makes it much worse. Alexandra, you are the first person I’ve seen to mention that this works for them also. :-)

Hi Sarah,
I’m thinking about doing the Elemental Diet to treat my SIBO. Rifaximin and herbal antibiotics haven’t worked. But I’m worried because the Elemental formulas have ingredients that are disallowed on the AIP.

Vivonex has soybean oil, cornstarch and maltodextrin from corn
Peptamen has soybean oil, soy lecithin, maltodextrin, hydrolyzed whey protein from milk, and cornstarch
Vital 1.5 has maltodextrin, whey protein hydrolysate, and canola oil.

Do you have any recommendations for this? Perhaps the Vital 1.5 is the better option since it doesn’t have soy? Perhaps the homemade formula is the way to go?

Thank you,


Any suggestions for enticing my son to eat? He is 7 years old and has had abdominal pain for nearly 6 months. I am currently waiting on the breath test results for SIBO, but in the meantime I am trying to implement a low fodmap diet per his doctor. Unfortunately, this child will only eat pancakes or occasional pizza. Or McDonalds chicken nuggets (blecth). Will not touch anything else, and goodness I have tried every approach imaginable. Dinnertime = stress time, for everyone in the family. Help!

Hi there,
Thank you for all your work, I appreciate it. Question: I believe I suffer from SIBO. I’ve been recently doing whole 30 and am noticing bloating from Potatoes, cashew, and sweet potatoes. I also have chronic constipation, which I assume is also an indicator. But to compound things, I also have histamine issues – so I struggle with probiotic foods, bone broth, vinegar, lemon, etc. So what can I do? Just a low carb/high fat diet? Anything else I should be doing? Oh, and I have developed numerous food allergies and intolerances, and it seems coconut is one of those foods, so no antimicrobial benefits there either. Any suggestions? Thank you for your help!

I have the exact same issues – big issues with high histamine foods (which SIBO can make much worse, as the fermentation of carbs in SIBO releases lots of histamine), food intolerances (same as you, coconut). I have been doing a low histamine diet for a year, but because I didn’t address SIBO directly, I’ve been getting sicker. With SIBO, low carb, high fat seems to be the only logical answer. I am trying the Fast Tract diet to track carbs and it’s helped my histamine issues alot by addressing bacterial overgrowth. I think once sibo is under control, the histamine will come in line more too, and as the gut heals, you will be able to tolerate ferments more, and then be able to heal more. I also have psoriasis, and sibo unchecked/high histamine has been making that so much worse as well. What a mess. But I think addressing the SIBO through diet is the first order of business.

Hi there,
After a long road, I’ve been diagnosed with SIBO, given two rounds of antibiotics and probiotics, tested again and nothing has worked. Methane levels are as high as usual. I’ve also tried gluten free, Fodmaps and all sorts of diets and nothing was worked. In the meantime Im still deficient and miserable. Any help/advise will be much appreciated.

If you haven’t tried them yet, Sarah recommends the GAPS or SCD diet for treating SIBO. It is also important that you’re addressing whatever caused the SIBO (poor diet, chronic stress, altered gut motility, etc) in the first place or recurrence is likely. Some studies have shown better results when using herbal antimicrobials over traditional antibiotics so that may be something to explore as well. With SIBO, it’s also important to address biofilm, which can be done using biofilm disruptors. Of course, it’s important to discuss this with your healthcare provider. -Kiersten

[…] albeit worrisome episodes. After examining my food diary in details, I decided to go low starch/ GAPS + AIP, I suspected SIBO (small intestine bacterial overgrowth) was the culprit. After 6 weeks of basically no starches, and severe adrenal fatigue, I was able to gradually add them […]

Sigh. In reading this I know that my *modified* AIP diet is not enough. I have a great Doc who says I need to remove tons of foods but refuses to tell me exactly what to eat bc he says I need to find the foods that work for me. I have already been diagnosed with Hashimoto’s disease, and have the MTHFR-c677t mutation. I also have endometriosis, PCOS, POTS, and fairly significant Candida overgrowth. I was doing great on my modified AIP (finally removed nightshades and it made a huge difference) but I ended up with pneumonia and had to take very strong antibiotics and steroids. I fell off my clean diet (not like others fall off-I started eating starches & sugars that “comply” with my diet regulations) and I’m feeling confused as to what to eat now. With all of these diseases and such I know I need a lot of diet restrictions but what do you suggest? When I eat something that is not perfect it causes such severe pain in my brain stem that it is crippling, as well as, GI issues and typical systemic Candida issues. I just keep going bc I have 2 kiddos so I’m living in the crazy condition where I would honestly prefer to never get up most days but that’s just not an option. Do I need to adhere to the complete AIP if my Hashis is in remission but my gut lining is permeable and Candida and endometriosis are out of control? I take Nature-Throid which works wonders for my Hashis.

A full AIP diet (and lifestyle) can work wonders for healing the gut, but it would likely benefit you to address the candida overgrowth as well. -Kiersten

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