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  • Writer's pictureMarissa Mekelburg MS, RDN, CLT, HHP

Top 5 Root Causes of IBS That You Should Know About

Tree in the middle of green pasture

In a previous post I discussed how IBS is defined as a medical diagnosis, why it can be hard to actually treat IBS and why you are doing yourself a disservice by accepting an IBS diagnosis and not continuing to look for the underlying reason for your IBS.

While everyone is unique and their underlying cause for IBS symptoms will be different, today, I would like to share with you five of the most common root causes that I see in my “IBS” clients.

What is a “root cause” and why is it important?

As I mentioned previously, it’s important to keep in mind is that IBS is a diagnosis or label that is given to someone who experiences a certain set of symptoms and is not in and of itself a cause or explanation for these specific symptoms. Treating IBS symptoms may provide short term relief but without getting to the underlying cause, your symptoms are bound to come back and depending upon the reason for the symptoms, chances are will progressively worsen.

Think of it like this – if the check engine light comes on in your car and you go to the mechanic – do you want them to just turn off the light or do you want them to figure out why the light came on in the first place, fix that problem and have the light go off by itself? I think most of us would choose the latter.

Ten people can have the same diagnosis, similar symptoms but entirely different root causes (or combination of causes) which is why one size fits all protocols don’t work and why you need to know what your root cause is. While this list is far from exhaustive, these are some of the most common root causes that I see in my practice working with those that have been diagnosed with IBS.

Root Cause #1 – Food Sensitivities/Intolerances

Food sensitivities are different from food allergies and are probably one of the most under addressed areas of modern medicine yet can be present in up to 30-40% of the population (although not everyone with a food sensitivity will present with IBS symptoms). In a nutshell, a sensitivity occurs when the body’s immune system overreacts to food (or chemicals like MSG, caffeine, food dyes etc.) and releases chemicals that cause inflammation and/or pain in the body. (1) Sensitivities can be difficult to identify because they can occur up to 72 hours after eating the offending food and many are dose dependent (meaning that a small amount may not create a reaction, but a larger amount will). Common foods that can create issues are gluten, dairy, eggs, corn and soy but a person can be sensitive to ANY food including ones that are considered healthy or anti-inflammatory like salmon, olive oil, turmeric or spinach and many times, a person will be sensitive to more than one food.

Food intolerances are different from a food sensitivity as they do not involve the immune system and are most commonly caused by a lack of appropriate enzymes to digest certain foods. An example of this would be lactose intolerance, which is very common and is caused by the body’s reduced or absent production of the enzyme lactase which is what breaks down the sugar in milk called lactose. When there isn’t enough lactase, lactose remains undigested and passes into the large intestine which creates an osmotic effect increasing fluid into the large bowel and results in pain, gas and diarrhea. (2).

Root Cause #2 – Increased intestinal permeability (aka “leaky gut”)

Leaky gut and food sensitivities often go hand in hand. The lining of the small intestine’s job is to act like a gatekeeper separating the inside of your intestines from your bloodstream and controlling what gets access into your blood. Normally only nutrients from fully digested food such as vitamins, minerals, amino acids etc. are allowed to cross the intestinal lining and get into the bloodstream and things like bacteria and undigested food particles (macromolecules) are kept out.

With leaky gut, there is damage to the lining of the intestinal tract and it becomes more permeable meaning that the gates are more open between the intestine and bloodstream and the things that are normally kept out, can now sneak through. Think of it like leaving the front door of your home wide open and inviting burglars in. Once these pathogens, toxins or macromolecules of food are in the blood, your immune system goes on alert and creates an inflammatory immune response which is what leads to symptoms.

Some common causes of leaky gut can be frequent antibiotic use, medications (such as NSAIDs, steroids, chemotherapy etc.), autoimmune disease (like Celiac disease), damage from bacterial toxins from conditions like small intestinal bacterial overgrowth (SIBO) and undiagnosed food sensitivities.

Root Cause #3 SIBO (Small Intestinal Bacterial Overgrowth)

Bacteria are normally present throughout the entire GI tract but in various amounts. The small intestine when compared to the large intestine has considerably less bacteria living there and some of the types of bacteria are different from those in the large intestine. SIBO occurs when there is an increased number in normal bacteria and/or abnormal type of bacteria in the small intestine (3). For most, SIBO is an overgrowth of various types of bacteria that should normally be found in the large intestine. (4)

Most common symptoms of SIBO include:

  • Abdominal pain/discomfort

  • Bloating and abdominal distention (many times within one hour of meals)

  • Diarrhea, constipation or alternating between the two

  • Gas/belching or reflux after meals

  • Weight loss and nutritional deficiencies (in severe cases)

SIBO also has sub types: diarrhea dominant, constipation dominant or alternating between the two.

Sound familiar? That would be because some studies indicate that as many 80-85% of those diagnosed with IBS have underlying SIBO (4,5). Yet SIBO remains largely underdiagnosed due to people not seeking care for their symptoms (or accepting an IBS diagnosis and not digging deeper) or because many doctors are either not familiar with SIBO or are unaware of how common this condition can be in those diagnosed with IBS.

Root Cause #4 Dysbiosis of Gut Microbiome

Our GI tracts contain a complex ecosystem of over 100 trillion microbial cells that influence human physiology, metabolism, nutrition and immune function and is referred to as our “gut microbiome” (6,7).

Recent research into the gut microbiome shows that the gut microbiota can interfere with normal intestinal functions, can affect intestinal motility and influence mucosal inflammation which may lead to or exacerbate IBS symptoms (7). Some recent studies show that up to 83% of those with IBS have abnormal fecal biomarkers and 73% have intestinal dysbiosis (11) Dysbiosis, which is often due to antibiotic use, is a lack in number or diversity of beneficial bacteria which can lead to the onset of IBS type symptoms and unfortunately, just one round of antibiotics can impact and alter the gut flora.

Root Cause #5 Gut Infections/Post Infectious IBS

Post infectious IBS is when IBS symptoms occur after having acute gastroenteritis (inflammation of the stomach and intestines as a result of bacterial or viral infection) and symptoms are believed to be related to persistent sub-clinical inflammation, changes in intestinal permeability and alteration of gut flora. (8)

Some common infections that I see in my practice are bacterial such as Heliobacter pylori (h. pylori) and Clostridium difficile, fungal like candida albicans or even parasites. Gut infections can occur from overseas travel, from digging in dirt in a garden, food poisoning, from an overly affectionate pet or caring for farm animals. Prior use of antibiotics can be a risk factor and contribute to overgrowth of Candida or SIBO (10) since they disrupt the microbiome by killing off not only the bad bacteria but also the good which creates an environment suitable to overgrowth and opportunistic pathogens. (10)

What Next?

You may be wondering at this point how in the world are you able to figure out if one (or more) of these common root causes is something you have?

The answer? Fortunately, all of these root causes can be discovered by working with a functional medicine/nutrition practitioner who will utilize a thorough assessment and health history to determine what testing needs to be done and will be proficient in interpreting the results to create a health re-building plan tailored just for you.

In the meantime, I really hope that you can now see why it is so important to keep looking for the root cause for IBS.

If you would like to learn more about how I can help, get started by scheduling an initial visit.


1. Food Allergy in Irritable Bowel Syndrome: The case of the non-celiac wheat sensitivity World J Gastroenterol. 2015 Jun 21; 21(23): 7089–7109.

Published online 2015 Jun 21.

2. The FODMAPs Approach — Minimize Consumption of Fermentable Carbs to Manage Functional Gut Disorder Symptoms By Kate Scarlata, RD, LDN Today’s Dietitian Vol. 12 No. 8 P. 30

3. Gastrointestinal bacterial overgrowth: pathogenesis and clinical significance

Amit H. Sachdev, Mark Pimentel

Ther Adv Chronic Dis. 2013 Sep; 4(5): 223–231.

4. Small intestinal bacterial overgrowth syndrome

Jan Bures, Jiri Cyrany, Darina Kohoutova, Miroslav Förstl, Stanislav Rejchrt, Jaroslav Kvetina, Viktor Vorisek, Marcela Kopacova

World J Gastroenterol. 2010 Jun 28; 16(24): 2978–2990. Published online 2010 Jun 28.

5. Small Intestinal Bacterial Overgrowth: A Comprehensive Review

Andrew C. Dukowicz, Brian E. Lacy, Gary M. Levine

Gastroenterol Hepatol (N Y) 2007 Feb; 3(2): 112–122.

6. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ

Caitriona M. Guinane, Paul D. Cotter

Therap Adv Gastroenterol. 2013 Jul; 6(4): 295–308.

7. Gut microbiota role in irritable bowel syndrome: New therapeutic strategies

Eleonora Distrutti, Lorenzo Monaldi, Patrizia Ricci, Stefano Fiorucci

World J Gastroenterol. 2016 Feb 21; 22(7): 2219–2241. Published online 2016 Feb 21.

8 Post-infectious irritable bowel syndrome

Marroon Thabane, John K Marshall

World J Gastroenterol. 2009 Aug 7; 15(29): 3591–3596. Published online 2009 Aug 7

9. Gut Reaction: Environmental Effects on the Human Microbiota

Melissa Lee Phillips

Environ Health Perspect. 2009 May; 117(5): A198–A205.

10. Antibiotic treatments and microbes in the gut.

Macfarlane, S.

Environ Microbiol, 2014 April; 16(4), 919-24

11. Irritable bowel syndrome, inflammatory bowel disease and the microbiome.

Major, G., & Spiller, R.

Current Opinion in Endocrinology, Diabetes, and Obesity, 2014 Feb; 21(1), 15–21

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