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5 Causes of IBS Your Doctor May Not Be Looking For


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causes of IBS
Gluten sensitivity and other food intolerances are common causes of IBS.

This article was originally published in 2015 and has been updated in November 2018 to reflect the latest research.

Do you have gas, bloating, abdominal pain, and stool issues? Up to 20 percent of the U.S. population suffers from irritable bowel syndrome (IBS), a condition that adversely affects daily life. Instead of digging deeper to identify the underlying cause(s), conventional medicine typically offers medications to suppress gut symptoms. Read on to learn about five lesser-known causes of IBS that you may not be looking for.

Irritable bowel syndrome doesn’t have to be a lifelong sentence. Learn about five underlying causes of IBS you might not be looking for to help heal the gut from the inside out.

How Doctors Diagnose IBS

IBS is the most common functional gastrointestinal disorder. Yet it’s poorly understood—not only by those who suffer from it but also by many clinicians who try to treat it. (1) Symptoms of IBS include gas, bloating, and abdominal pain, accompanied predominantly by constipation, diarrhea, or both. Those afflicted report lower quality of life and activity levels and call in sick twice as often as the general population. (2) Depression and anxiety often accompany IBS, most likely through the gut–brain axis connection between the enteric nervous system of the GI tract and the central nervous system.

Diagnosing IBS isn’t straightforward. If you’re experiencing the above symptoms but you don’t have a more definable GI issue like inflammatory bowel disease (IBD) or GERD, then IBS might fit the bill.

Over the years, diagnostic criteria have evolved, but IBS is now generally defined as recurrent abdominal pain at least three days per month in the previous three months, associated with two or more of the following: (3)

  • Improvement with defecation
  • Onset associated with change in stool frequency
  • Onset associated with change in stool consistency
Finding the root cause of IBS isn’t always an easy or quick road. But there is hope for those suffering. I believe one of the greatest allies someone hoping to heal from it or any other chronic condition can have in their corner is a health coach. Coaches work alongside Functional Medicine practitioners to help people finally heal. If you’re passionate about helping others find health and happiness, a career in health coaching may be the right fit for you. Find out how to become a health coach.
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IBS Medications Aim to Tame, Not to Treat

Not that long ago, IBS was dismissed as a psychosomatic disorder that was “all in your head.” Fortunately, it is now recognized as a legitimate gastrointestinal disorder, although it’s often poorly managed. Current treatments focus on alleviating the symptoms of IBS instead of actually fixing the underlying problems—but that’s a common theme in conventional treatment of modern chronic diseases. Medications prescribed for IBS include:

  • Antidiarrheals
  • Anticholinergic or antispasmodic drugs
  • Laxatives
  • SSRIs
  • 5-HT3 antagonists
  • Mast cell stabilizers (also used to treat asthma)

But those who use these IBS medications report low satisfaction, with little relief from the condition, and many of these drugs induce side effects that are similar to IBS symptoms themselves! (4, 5)

Treating gastrointestinal symptoms without addressing the underlying gut issues is akin to repeatedly placing buckets underneath water dripping from the ceiling. The floor below may stay dry, but that won’t fix the hole in the roof. Over time, the leaky roof could lead to additional problems, like mold and structural instability.

5 Causes of IBS You May Not Have Considered

In order to properly treat IBS, you’ll need to do some investigating to determine the cause. This article will summarize five causes of IBS that you may not be looking for—but should be.

1. Gut Dysbiosis

Ever-growing research links the gut microbiome to bone health, heart health, autoimmune disease, thyroid health, and more. It should be no surprise, then, that IBS is directly related to gut dysbiosis, a change in the composition of the gut bacteria. Up to 83 percent of IBS patients have abnormal fecal biomarkers, and up to 73 percent have intestinal dysbiosis. (6) Specifically, those with IBS tend to have decreased levels of “good” bacteria, such as Lactobacilli and Bifidobacteria, and increased levels of harmful strains such as E. coli and Clostridia. (78) An increased ratio of Firmicutes-to-Bacteroidetes (two major classes of bacteria) is also common. (9)

Success in treating IBS with prebiotics and probiotics is further evidence that gut dysbiosis plays a role in IBS. A recent article reviewed 24 randomized placebo-controlled probiotic trials, the majority of which showed benefits of treatment. (10) Beneficial probiotic strains included B. animalis, L. rhamnosus GG, B. infantis, B. longum, and L. acidophilus. (11, 12, 13) Prebiotics, which act as food for the microbiota, can also help establish beneficial bacterial. (14, 15, 16)

Another strategy that can correct gut dysbiosis is a low-FODMAP diet, which eliminates foods containing certain carbohydrates that feed intestinal bacteria. (1718, 19) This method may help get the beneficial-to-harmful bacteria ratio back under control, but it works best as a short-term solution that is then followed by prebiotic/probiotic treatment. (20, 21, 22)


Small intestinal bacterial overgrowth (SIBO) is a special subset of gut dysbiosis in which the small intestines harbor an abnormal number of bacteria. Compared to the colon, the small intestine should have a bacterial concentration that is considerably lower. Bacterial overload in the small intestine can interfere with digestion and nutrient absorption.

SIBO may be present in up to 80 percent of IBS patients, although a recent meta-analysis reported a huge range of estimates (between 4 and 78 percent) across 50 studies. (23) Part of the reason for the discrepancies is non-uniform IBS diagnosis, and the other part may be variations in SIBO diagnosis. I prefer the methane breath test over jejunal aspirate and culture, the conventional testing approach.

Antibiotics that are used to treat SIBO, like rifaximin, can also be effective for treating IBS, further evidence that SIBO may be underlying some cases of IBS. (24, 25) Or, SIBO may follow IBS incidence, especially if a person with IBS begins taking PPIs (acid-blocking medications) for indigestion. One of the many dangers of PPIs is the development of SIBO. (26, 27)

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3. Gut Permeability

The GI tract is lined with a single layer of tightly packed epithelial cells designed to keep pathogens and other unwanted species out of the bloodstream. If the barriers between cells become permeable, undigested protein molecules and bacterial toxins can pass through and trigger immune reactions and inflammation.

Leaky gut and associated low-grade immune activation affect between 12 and 50 percent of people suffering from IBS. (2829, 30) Low levels of E-cadherin, a protein involved in regulating gut permeability, have been reported in IBS sufferers who experience diarrhea and/or constipation. (31)

Supplements that can help reestablish the intestinal barrier include:

  • L-glutamine
  • MSM and quercetin
  • N-acetyl glucosamine
  • Mucin
  • DGL slippery elm
  • Marshmallow
  • Chamomile
  • Cat’s claw

GI-Revive contains several of these in an effective blend. Supplementing with probiotics can also help repair gut permeability. (33)

4. Gut Infection

Gut infections are another lesser-known cause of IBS. Many studies have confirmed a link between a single episode of bacterial gastroenteritis and future development of IBS. (34, 35, 36) Parasites such as B. hominis, Giardia spp., E. histolyticaDientamoeba fragilis, and Trichinella spp. have also been correlated with progression of IBS, although causation has not yet been confirmed. (37, 38, 39)

Modern lifestyle has compromised the gut’s ability to resist infections from pathogenic bacteria and parasites. (High levels of stress, for instance, combined with factors such as the Standard American Diet, can easily lower our immunity.) Gut permeability, gut dysbiosis, and high stomach pH from chronic PPI use create more opportunities for pathogens to overwhelm or bypass the gut’s immune defenses.

5. Non-Celiac Gluten Sensitivity and Other Food Intolerances

The medical field once mocked non-celiac gluten sensitivity (NCGS), but the condition is slowly gaining acceptance even in conventional medicine. (40) Many of the symptoms—gas, bloating, abdominal pain, and changes in stool patterns—are indistinguishable from IBS, so NCGS can be difficult to identify. Brain fog and fatigue following gluten consumption are also very common.

In IBS patients, I see a number of other food intolerances, such as:

  • Dairy
  • Eggs
  • Peanuts
  • Seafood
  • Yeast
  • Soy

A large review of over 73 studies “confirmed that food allergy and intolerance should be considered as an underlying pathology for IBS.” (41) But bear in mind that food intolerances themselves are often symptoms of deeper causes like SIBO, gut infections, and/or gut permeability.

The cheapest tool to determine food intolerances is an elimination diet, which I outline in depth in my book The Paleo Cure.

What’s Your Experience with IBS?

IBS can be an unpredictable and even debilitating condition. Finding the root cause is not always an easy or quick road, but neither is a lifetime of symptom-suppressing medications with additional side effects.

In my practice, I have seen patients who have suffered from this condition for 20 years recover after we identify and address the underlying causes of IBS outlined above and fix their diets.

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  1. I have lived with IBS for 3 years. Was told by my DR. more fiber and less stress. Funny thing is I am under no stress, More fiber really gets the IBS acting up big time. I stay constipated. He gave me Linzess 290mg for that plus I am on a probiotic and 40mg Prilosec twice a day. Had H.pylori and a none functioning Gallbladder at the same time. the removed the gallbladder and that’s when everything went crazy. he did endoscope and colonoscopy and said ge junction and lining of stomach was inflamed that’s when I was given the Prilosec. then I kept sick and was none stop going to the bathroom and sick on my stomach and in pain. he then said you have IBS that was without running anymore test. this all happen over a span of 3 years. now he says “I THINK YOU ARE LACTOSE INTOLERANT” but has never run any test. he does not ever run the blood test he is suppose to run while you are taking the Prilosec to make sure my magnesium or potassium is not low. was having pain and spasm in my arms and my joints hurt and my legs it was my pharmaces who told me I was probably had low magnesium so he showed me the ones to try and within a couple of days the pain stops. My gastrologist does not seem to want to do anything he just says “I THINK” and tells you do this or do that and leaves the room you have to run after him to ask him questions. so I hope they come up with something. Anyone have any advice for me I could so use it.

    • Western Medicine doctors don’t look at the body as a whole. They don’t really know nutrition either. You would need a team to help you like an Integrative Medicine Gastroenterologist and perhaps a registered Holistic nutritionist to help you to feel better.
      You may have a bacterial overgrowth that needs to be diagnosed through a breath hydrogen test and then taking the necessary items to improve your digestion would be paramount. You’re not digesting your food well so you get an overgrowth of bacteria and this irritates the gut lining.
      You may need digestive enzymes, ox bile and probiotics. Getting a stool test done can help to figure out the mystery too! Western Medicine GI doctor’s don’t test the stools for an imbalance in gut flora only Functional/Integrative Medicine MD’s do.
      Hope this helps!

      • Also the Prilosec which i believe is an acid suppressor, a PPI (Proton Pump Inhibitor) is going to mess up your digestion as you need Hydrochloric acid to digest your food. You will have a real problem if you take any acid suppressing over the counter products. God created us to have HCL acid to break down our food in the stomach first if we don’t have this function, parasites won’t be killed either when they enter the stomach from our food.

    • Your pain/problem sounds just like mine. I can’t eat out. I can’t travel any more cause there aren’t bathrooms close enough and I get very sick and my back hurts and my brain works very slow. I lose my temper which I never do. It isn’t stress. The last 7 years I’v been in so much pain. My stomach is huge and I have lost weight. I have tried and done everything and I can’t get it figured out. Doctors don’t help. I’ve been through every test. They don’t even put a name to it. I just call it IBS. I’m so sick and tired of being sick and tired.

  2. I am still trying to figure out how I got Candida. 25+ years ago I went to Puerto Vallarta on vacation, ate some Ceviche in a restaurant, had intestinal cramping and pain. I saw my PCP who referred me to a GI doctor and that Dr. tried to perform a sigmoidoscopy on me back around 1992. I was literally screaming and in pain from him inserting the scope up my rectum. I vaguely remember seeing two Holistic doctors and taking Pao D’arco tea. I came across an invoice from one of them that mentioned something about probiotics….which I don’t think I took. Its hard to remember. But I do remember being diagnosed with Candida. I went on the Candida diet and I thought I was cured…..20 years later I saw a Functional Medicine doctor that did a thorough inspection of me with stool tests and blood work. She found Blastocystis Hominis in my stools. I am wondering why western medicine doesn’t think this is a threat?
    So what happened over that time, thinking I was cured, I drank wine excessively to reduce my anxiety. I know today that the chronic candida, drinking the alcohol, eating gluten, taking NSAID’s, advil (for menstrual cramps) all contributed to a severe leaky gut and my anxieties. Adrenal exhaustion, etc.
    I now barely hanging on for me life….as mainstream mediacine doesn’t acknowledge that a person can have Candida overgrowth…and it has spread into my tissues and I am severely nutritionally deficient…which has been affecting my liver function. I can’t take anything that feeds fungus, like B vitamins, which helps me to methylate things through the liver.
    I don’t know what to do anymore…and am so sad that the technology and explanation for something so simple as getting a parasitic infection would cause me my life. Back around the time when I was diagnosed with Candida, I came down with Chronic Fatigue Syndrome, EBV, and Cytomegalovirus (all diagnosed) I also had both of the Herpes viruses too. I was never breast fed, given antibiotics for various infections, acne, and MVP (mitral valve prolapse). Growing up in the 60’s, and 70’s I wasn’t fed a nutrient dense diet. If have one of the HLA genes (DQ-2) for gluten sensitivity. I ate a lot of Karo syrup on my waffles and pancakes.
    I am so so sad how things turned out for me. I guess I was just born at the wrong time…that’s my only explanation.
    I wish someone out there could help me but I think at this point there may not be any help.
    Thank you for being here to help others through your struggles….I am doing the same for others too!
    Blessings to you all.
    Chris, do you know to break through Candida Biofilm? I have hyphal fungus lining my stomach and intestines….I can’t seem to destroy it. Any suggestions? Please help. Perhaps Dr. Schweig might offer a suggestion too!

  3. I was told I had IBS 3 years ago. I have tried various anti-depressants, Bently, Accuputure, Hyponosis, Cognitive therapy, Fod-map diets, surgery to remove lesions with know relief.

  4. I have had IBS symptoms for more than 10 years, but have not been officially diagnosed because my doctor believes it’s purely “in the mind”.
    I’ve just had my water tested (because of these symptoms) and It apparently has very high levels of coliform bacteria and needs to be treated. This was also the case when it was last tested two years ago. I’m now wondering if it’s possible for coliform bacteria (and low levels of E.Coli) to cause chronic IBS/SIBO? I’m not finding much on that online, but it would be wonderful if fixing the water contamination could help.

    Thanks for all the helpful articles! It’s very heartening to find such a wealth of information on SIBO, IBS and general health.

  5. I thought I had celiac, but recently had the breath test for SIBO and it was positive. After doing some research, I decided to forego the antibiotics and go the diet, supplement, and functional neurologist route. Am better, but still have problems with too many bowel movements and some gut discomfort. I am doing the SCD (specific carbohydrate diet) with modifications for the foods I’ve tested positive for through allergy testing. Has anyone used the FODMAP diet for SIBO? I’m wondering how they compare.

  6. Hi,
    I suffered from IBS for more than ten years. Tried virtually everything mentioned in the article. Nothing worked. I have a BMI of 20 and excersise everyday.
    Stopped consuming refined sugar – that is absolutely everything and anything that has refined sugar – IBS stopped almost immediately and I am still completely free after three months. I do not remember ever feeling this well. My diet is very omnivore BT leaning to eating plenty of saturated fats, cheese, butter, cream etc. weight stays the same whatever I eat now that there is no refined sugar in my diet.

  7. Hi

    I am 43 and have had digestion issues for more than 20 years – getting steadily worse. I cut out gluten about 15 years ago, which I could never go back to now as the effects are so severe, but there is still quite a bad reaction to almost any food. Some foods consistently cause problems (like nuts, seeds, dairy, more recently even avocado, etc) so I avoid them. Other foods cause problems in combination with the rest of my condition (e.g. if I am tired or stressed). The only foods that seem to be safe for me at any time are vegetables, salads, and mung sprouts, so these do form a large proportion of my diet. Tofu is usually fine as well, so is quinoa, and white basmati rice if I don’t have it too often. Good diet for nutrients, but not so balanced and not great for weight – I am underweight anyway, which is not really improved when I eat a lot (I just feel more ill), but I do lose more when I eat too lightly.

    What I get is a sense of bloating (which feels much worse than it looks) either in my upper gut, or around and below the navel – sometimes one leading to the other. It is accompanied by a feeling of weakness, sometimes breathlessness, and often a tight ache round the back of my skull.

    I have tried several probiotics, which have not helped, and enzymes & bitters, which sometimes help a little bit but not much.

    Any thoughts on how to address this further?

    • My symptoms are remarkably similar to yours (except anxiety as well sometimes), and I am 48, and its been going on for 20-25 years, I had some CSDAP (or whatever its called) done, which found some dysbiosis, and I have been taking so many anti-microbials, and large doses of probiotics for months, now and still no improvement per se.

      It seems there are many underlying causes, and lot of current treatment protocols are either based on conjecture or theory rather than science, but sadly there is no other recourse than try whatever can be tried in the hope that something may work…

      • Thanks for sharing this TK. Since writing it, I have taken a new approach and it seems to be really helping.
        For years, I have been worried about all the foods I can’t eat and how my diet has been getting more and more limited. I did a lot of research about what could help (nothing did) and about what sorts of foods are the health-promoting – but some of them gave me bad symptoms.
        So I tried a different approach, really trying to listen to my body. I went on a very simple diet for a while, and found that in my case, it was raw fruits and vegetables and sprouts and sea vegetables that were really good for me and when I stuck to the diet, my problems were significantly reduced. Now I eat this diet – supplemented by a nutritional shake every day (and actually I think this is the only thing that is a problem for me in what I am eating now – I think because it is full of protein and fibre – I am using Living Fuel, but might switch soon to something like Green Vibrance without all the extra stuff).
        And what I found was good for my digestion is not what I would have thought. For example, nuts and seeds are supposed to be such a good natural source of protein and fat and nutrients – especially when sprouted, but my body just can’t deal with them. It is sad to be losing their nutritional value, but I guess I wouldn’t be benefiting from that anyway if my body was rejecting them.
        Hope this is useful.

  8. I struggled with IBS symptoms for seven years and it was progressively getting worse. Medications did not seem to help and even with a food diary, I was unable to pinpoint particular food sensitivities. Finally, a year ago, I tried the FODMAP diet. Bingo! As long as I avoid the foods on the list, I am symptom free! No meds! Wheat and corn are the biggest triggers, but several of the fruits and veggies on the list are problematic as well. The diet is restrictive but definitely worth it!

  9. Some people I know with IBS tend to eat very quickly and they don’t chew their food much either. While this isn’t an underlying condition, it certainly doesn’t help.

  10. I have Type 1 diabetes and suffered from IBS for years until I realised which foods were causing it for me. In my case it was chick peas and palm oil. I believe that many people who think they cannot tolerate wheat are actually unable to tolerate palm oil. As son as they give up commercially produced wheat products (cakes, biscuits, etc) and dairy (commercially produced ice cream), they also give up palm oil because most manufacturers use palm oil these days. Palm oil is a relatively new element in the Western diet, and its introduction coincides with the epidemic of “gluten/wheat intolerance”.

    • I have been diagnosed with MS in 2005. I have IBS, as well as colitis and kidney problems. I think some how they all just tiee together. But I have found that since I have given up dairy, it has made a big difference. Also I can’t eat fast foods. I try to eat healthy!

  11. Hi, lve got Crohns and lve started on a gluten free diet been on it for 7 weeks and different supplements that my Holistic Doctor said to take as lve got leaky gut, Crohns and early parkinsons. lve been on Gluten free for 7 weeks and had loose stools all that time. lve had to reduce my Crohns medication which now im off, My doctor said with all the herbs and gluten free diet lm on my inflammation should heel and bowel and leaky gut be under control. lm just not sure about all this as lve had a few pains and am running to the toilet more since lve stopped taking sulfasalazine. Dont know if l should go back on my medication or wait and see what happens. How long does it take for loose stools to go back to normal. Regards Gaye

  12. The doctors talked to me 5 minutes and decided it was IBS, telling me there is nothing to do, just continue to avoid the food that gives you the symptoms… My Naturopath thinks it’s Candidadis infection and / or SIBO, and I’ve been doing both diet simultaneously (for 3 years now) and it really helped but the moment I try to reintegrate some of the foods (ie fruits, even the ones the SIBO accepts) it all comes back. My feeling is leeky gut, because I don’t digest food properly (undigested food in my stools) and even after a really good meal, well balance, no intolerance food in it, lots of lean protein, I feel weak and starving and loose muscle mass… The only thing that as helped so far is taking the Intestinal Pack form Metagenic that helps restore gut permeability. I want it to be done with. I want to be healed! Any ideas?

    • I have the same problem and I am pretty sure it’s leaky gut and SIBO. I also suspect low stomach acid and dysfunctional enzymes from pancreas and gall bladder (that has been confirmed by stool analysis). The only thing that seems to help is avoiding most fats and anything processed. I sometimes take probiotics and digestive enzymes but I should do it more regularly I think. There are definitely some foods that aggravates this condition, even some fruits and vegetables (ripe bananas, some night shade veggies). Green apples help with my acid reflux.

  13. My gastroenterologist is Head of the Dept in our only hospital in Grass Valley CA.
    He refused to even try to treat my very severely painful gut, not once but twice.
    I am so disgusted by American doctors, I can barely contain it. I think they want us to die, seriously.

  14. I have been diagnosed with IBS. My doctor has suggested no wheat or gluten…which I have been following for months now. He also has suggested certain fruits and vegetables I should not eat…..like apples, watermelon, peaches, cherries, cauliflower, beans and lentils , to name a few. He also has me taking a papyaya enzyme. I’m on cholestyramine . Once a day. I get a lot of pain in my right side only and recenlty had a CT f abdomen, with no findings. I’m now scheduled for colonoscopy. I’m not really sure what’s going on. I really don’t like meds and squally get the prescription filled and never open the bottles…..

  15. I have found (by trial and error) that when my IBS flares up, probiotics help to diminish or eradicate my symptoms…at least for a while. I have also learned to avoid my triggers: stress, coffee, high-fat foods, and overeating. I was on SSRIs for a while, but that didn’t seem to help.

  16. Suffering from ibs for almost 10 years. Sugar definitely is not good for me. Taking a lots of supplements , oregano oil helps. Read a book of jini pathel and her protocol of ibs she recommends going for two weeks on a liquid diet to heal the intestines. If anyone knows about that please let me know, also looking for a good naturopath in the Miami fl area.

  17. Two years ago my family went on a trip out of the country to work in an impoverished area. I got severely ill there and thought we cured it with antibiotics. After coming back, I continued with fever, chills, and gut pain and was misdiagnosed with IBS from a GI doctor who wouldn’t take the time to listen. After getting severely sick again after 7 months of little help, an infectious disease doctor determined that I had e-coli from the water. We fixed this with Xifaxan, but I continued to have unexplained gut pain. A new GI doctor diagnosed me with SIBO and leaky gut. We have done multiple treatments with Xifaxan but the SIBO returns a month later. I have started working with a functional medicine doctor who found that I also have dysbiosis, candida, and was having malabsorption issues. He has had me on heavy duty probiotics, HCL and digestive enzymes, glutamine, fish oil, magnesium, and vitamin D and B. We have done anti-microbial and homemade elemental diet treatment for the SIBO, but I have relapsed. We are now seeking a more specialized functional medicine doctor that can do more extensive diagnostics to determine a more extensive protocol that prevents relapse. We will persist until I beat this!

    • Tiffany,

      I also get better with herbals but then a month later I seem to relapse as well. Can you keep us updated with your treatment? Love to hear what they find.

  18. I have IBS-C (suspect SIBO based on symptoms) and have for more than 20 years. The only thing that relieves the pain and bloating and helps me to go is magnesium citrate. Until I can figure out how to get rid of IBS, I couldn’t live without magnesium. I noticed recently after taking a round of antibiotics for an ear infection that my IBS symptoms stopped. I can’t get my doc to prescribe a round or Rifaximin, so I’m going to try the herbal route. Thanks for all the information you provide Chris and commenters!