Top 5 Causes of IBS and How They Relate to Leaky Gut

In Part 4 of her series on Leaky Gut, Dr. Doni starts to explore the causes of Irritable Bowel Syndrome, a condition that is inextricably linked to Leaky Gut.

Part 4 of Dr. Doni’s Series on Leaky Gut

leaky gut, Irritable Bowel Syndrome, IBS, intestinal permeability, food sensitivities, digestion, indigestion, inflammation, fructose malabsorption, lactose, blood sugar, healing leaky gut, microbiome, probiotics, yeast overgrowth, lactose intolerance, dysbiosis, SIBO, natural healthIn the first three parts of this series we have taken a broad look at Leaky Gut: what it is, how to test for it and how to treat it. Here are the links if you would like to catch up:

However, things aren’t quite that simple with this most complex of conditions that has a whole raft of possible causes and influences. One condition that plays a huge part in Leaky Gut is Irritable Bowel Syndrome or IBS. This interconnected condition is in itself, very complex with multiple symptoms and multiple potential causes. Many people suffer with IBS without necessarily realizing it. And, even if they are aware of it, they don’t always know what it means.

Many people don’t realize that this connection between IBS and Leaky Gut exists. As we saw in part one of this series, Leaky Gut happens when the cells of the intestinal lining are unhealthy, creating gaps that allow undigested food to ‘leak’ through the intestinal wall and trigger the immune system. IBS is diagnosed when a person has digestive upset—including things like constipation, diarrhea, and stomach cramps—but without an acute infection or inflammatory bowel disease.

So how are the two related? Well, it’s a tricky one because, on the one hand, IBS can cause Leaky Gut but on the other, Leaky Gut can also cause IBS!  The inflammation and digestive disturbances associated with IBS can damage the intestinal lining, and a less-than-healthy intestinal lining makes it harder for the digestion to work optimally. This causes a confusing ‘chicken and egg’ situation where it’s hard to tell where the problem started. This in turn, makes it difficult to diagnose and treat the root cause of your problem.

For this reason, it’s essential we do the right tests that will lead us to the right diagnosis and the right healing solution for your problem.

To help untangle this conundrum, over the next two installments of this series I will take you through the ten most common causes of IBS and look at how they affect Leaky Gut and how to test for and treat each of them. In this post, we’ll look at the top 5 causes:

  1. Lactose intolerance
  2. Fructose malabsorption
  3. Dysbiosis – when your healthy bacteria are out of balance
  4. Yeast overgrowth
  5. SIBO (small intestinal bacteria overgrowth)

And in the next post, we’ll tackle 5 more root causes:

  1. Kinetic issues, like constipation
  2. Food sensitivities
  3. Histamine intolerance
  4. Maldigestion – not having the right amount of acids or enzymes to digest food properly
  5. Stress

The Top 5 Causes of Irritable Bowel Syndrome (IBS)

  1. Lactose intolerance

Lactose intolerance means that your body is not able to digest lactose—the sugar that occurs naturally in milk products (milk, yogurt, cheese, ice cream). It is a common, yet often undiagnosed, cause of IBS.1 Undigested lactose is fermented by bacteria, producing gas and attracting water to it within the intestines which leads to bloating, nausea, rumbling, and potentially vomiting, diarrhea or constipation. Lactose intolerance can be genetically determined or caused by other intestinal issues such as infections.

The Link to Leaky Gut
Leaky Gut decreases your ability to digest lactose making lactose intolerance more likely to occur when Leaky Gut is present. Not only that, but lactose intolerance makes Leaky Gut worse (especially if you are still eating lactose) because when the lactose is fermented, it makes your gut more leaky.

The Test
A simple breath test analyses your breath after you have consumed lactose to determine whether or not the lactose was digested. You breathe into a tube and the gases in your breath will indicate whether lactose is being fermented in your gut instead of being digested. It can be performed by a gastroenterologist or a naturopathic doctor.2

The Treatment

  1. Fructose Malabsorption

Fructose, the natural sugars in fruit and certain vegetables, is digested by enzymes made by the cells that line the intestines. Any fructose that is not digested will not be absorbed through the intestinal lining as it should be and will instead draw water toward it leading to gurgling, bloating, bowel changes, and potentially brain fog, headaches, and/or fatigue.

Fructose malabsorption means you are not able to digest and absorb fructose properly. Approximately 30% of us have a genetic variation that means we are less able to digest fructose. You can read more about genetic variations here.

The Link to Leaky Gut
We are less able to digest, and therefore absorb, fructose (and other sugars) when the intestinal cells are damaged (Leaky Gut). Then any undigested sugars are fermented, leading to further damage to the intestinal lining.

The Test
A simple breath test that determines whether you have fructose malabsorption by testing the gases in your breath after consuming fructose. This test is available through some gastroenterologists and naturopathic doctors.

You could also do a trial elimination of fructose from your diet and see if you feel better.

The Treatment

  • Decrease or avoid foods that contain a high amount of fructose.
  • Avoid ‘FODMAPs’ (Fermentable Oligo-Di-Monosaccharides and Polyols). These are foods that contain fructose or fructans including: fruit, high fructose corn syrup (HFCS), lactose, wheat, garlic, onion, inulin (a fiber often found in probiotic supplements), beans, lentils, soy, sugar alcohols which are commonly used as sweeteners such as mannitol, sorbitol, and xylitol.3
  • Heal Leaky Gut. Because Leaky Gut is an underlying cause of fructose malabsorption, healing Leaky Gut is an important treatment. You can learn more about how to do this in part three of this series.
  1. Dysbiosis

This is when the healthy bacteria living in your large intestines are out of balance.
We call this your ‘microbiome’—a local community of bacteria living in your large intestines where it creates nutrients and vitamins, and keeps not only your colon, but also, we now know, your whole body healthy. An imbalance of healthy bacteria is associated with autoimmunity problems, diabetes, heart disease, kidney disease, anxiety and depression, as well as weight gain and cancer.

The Link to Leaky Gut
One of the most common causes of dysbiosis is the overuse of antibiotics, which kill the healthy bacteria that are present in the gut; antibiotics are also a cause of Leaky Gut. Another common cause of both IBS and Leaky Gut is an intestinal infection, such as a parasite, virus or bacterial infection. Whether the problem is antibiotics or an intestinal infection, a vicious cycle develops that perpetuates both the symptoms of IBS and the conditions related to Leaky Gut. 4

The Test
More and more tests are being developed to give us the ability to understand the state of your microbiome and they involve a stool analysis.

Your gastroenterologist will not generally order any of these tests. However, a naturopathic doctor can order a Genova GI effects panel for you which measures bacteria based on a DNA probe. The websites American Gut Project and uBiome offer home tests.

The Treatment
Treatment depends on whether you have too few good bacteria or too many of the wrong bacteria. The aim of treatment is to eliminate unwanted bacteria and reintroduce those that are known to bring balance to the world inside your gut.5 This process is relatively complicated and undefined, so working with a practitioner is imperative however treatment will involve one or other the following supplements (or a combination of the two:

You can click here to read more about probiotics.

  1. Yeast Overgrowth

When the microbiome is disrupted (often from the use of antibiotics) and a high-sugar diet is consumed (yeast lives on sugar), then an overgrowth of yeast can occur in the intestines. When this happens bloating, gas, and intestinal discomfort are common, as are symptoms in other areas of the body such as fatigue, brain fog, skin rashes, and mood fluctuations. This is because yeast releases aldehydes (oxidized alcohols that must be detoxified by your liver and can cause you to feel worse until they are processed out) into your body and can overwhelm your body’s ability to detoxify them.

The Link to Leaky Gut
While yeast overgrowth can cause IBS, it can also cause Leaky Gut which, in turn, makes you more susceptible to yeast overgrowth. This is because the yeast compromises the health of the gut lining—healthy bacteria in the intestines require a healthy gut lining in order to survive and to prevent yeast and abnormal bacteria from thriving. Without a healthy lining, you are left vulnerable to overgrowth of yeast.

The Test
There are many things we can test for that can tell us whether yeasts are overgrowing in the intestines. They include urinary organic acids, blood antibodies, and yeast. While yeast can sometimes be identified by a gastroenterologist during an endoscopy or colonoscopy, if you suspect yeast overgrowth, a naturopathic doctor will be able to help you with the other (more reliable) forms of testing for yeast (urine and stool).

The Treatment

  • Anti-fungal medications that treat yeast (Diflucan and Nystatin for example)
  • Herbs that kill yeast (e.g.: Berberine extracted from Oregon Grape Root, garlic, oregano, pau d’arco)

We can use these herbs, alone or in combination, in gradually increasing doses to address yeast overgrowth but without triggering a “yeast die-off” response that can exacerbate the symptoms—a reaction caused by the aldehydes that the yeast releases as it dies.

It is important to work with a practitioner who can put together a comprehensive plan that includes healing Leaky Gut as well as addressing yeast overgrowth so that the yeast doesn’t simply return as soon as you stop the anti-yeast treatment. You can read more about yeast overgrowth here.

  1. SIBO (small intestinal bacteria overgrowth)

We mainly hear about the bacteria living in our large intestines (see cause #3 – Dysbiosis), but in the case of SIBO, the issue is an overgrowth of bacteria in the small intestines. This bacterial imbalance causes burping, belching, bloating, and intestinal discomfort. SIBO is found in close to 50% of patients with IBS.6

SIBO has several possible causes, most notably constipation, low stomach acid, and stress. SIBO also increases the likelihood that you’ll start reacting to more foods, both due to food sensitivities and to increased histamine reactivity. We’ll cover how all of these causes of SIBO are related to both IBS and Leaky Gut in detail next time.

The Link with Leaky Gut
As with dysbiosis and yeast overgrowth, when SIBO occurs, it causes increased intestinal permeability (Leaky Gut) because the disturbances caused by overgrowing bacteria cause damage to the intestinal lining. Then, as the intestinal lining is less stable, it makes it easier for the bacteria to survive where they shouldn’t be, and those bacteria can then leak through the intestinal lining triggering more inflammation and overwhelm throughout your whole body.

The Test
A specific breath test will tell us whether the levels of bacteria living in your small intestine are too high. You’ll ingest a sugar (lactulose) and then breathe into a tube every 20 minutes for anywhere between 90 minutes and 3 hours. Then your breath will be analyzed for methane and hydrogen, both of which are released when bacteria ferment sugar. This test is available through a gastroenterologist or naturopathic doctor.

The Treatment

A full protocol of treatments that addresses all the underlying causes, including:

  • Support for digesting food
  • Avoiding sugars and foods that are not easily digested or that are fermented by the bacteria
  • Ensuring regular bowel movements
  • Treatments to kill the excess bacteria whether with antimicrobial herbs (which is my preference) or antibiotics

I find that it is only when we set out to completely change the environment in your digestive tract that we can fully eliminate SIBO. If we just kill the bacteria, without addressing Leaky Gut or maldigestion, then SIBO will return. To that end, treating SIBO can take several months of diligence with your diet, digestive support, and treatments that disrupt the bacteria and re-establish them where you want them to be—your large intestines.

Closing Thoughts

As you can see, IBS is a complex issue and, as a result it can be difficult to figure out the root of the problem in order to put together an effective treatment program. Add to this the complications of its chicken and egg relationship with Leaky Gut and you can see it takes time and patience to finally get to the heart of the problem and start you on the path to health.

leaky gut, Irritable Bowel Syndrome, IBS, intestinal permeability, food sensitivities, digestion, indigestion, inflammation, fructose malabsorption, lactose, blood sugar, healing leaky gut, microbiome, probiotics, yeast overgrowth, lactose intolerance, dysbiosis, SIBO, natural healthNext time, we will look at the next five causes of IBS (kinetic issues, food sensitivities, histamine intolerance, maldigestion, and stress), the relationship they have with Leaky Gut and how you can test for and heal them. If you want to be sure not to miss it, you can subscribe to this blog and it will be sent straight to your inbox.

If, in the meantime, you feel ready to tackle your own Leaky Gut and would like my support, please check out my new treatment package specifically designed to help you heal your Leaky Gut. Alternatively, you can drop me a line using the contact form to ask about how else I might help you.

–Dr Doni
9th July 2015


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  2. Rana SV1, Malik A1. Breath tests and irritable bowel syndrome. World J Gastroenterol. 2014 Jun 28;20(24):7587-601.
  3. Halmos EP1, Power VA2, Shepherd SJ2, Gibson PR3, Muir JG3. A diet low in FODMAPs reduces symptoms of irritable bowel syndrome.Gastroenterology. 2014 Jan;146(1):67-75.e5.
  4. Donskey CJ1. The role of the intestinal tract as a reservoir and source for transmission of nosocomial pathogens. Clin Infect Dis. 2004 Jul 15;39(2):219-26.
  5. Barbara G1, Zecchi L, Barbaro R, Cremon C, Bellacosa L, Marcellini M, De Giorgio R, Corinaldesi R, Stanghellini V. Mucosal permeability and immune activation as potential therapeutic targets of probiotics in irritable bowel syndrome. J Clin Gastroenterol. 2012 Oct;46 Suppl:S52-5.
  6. Moraru IG, Moraru AG, Andrei M, Iordache T, Drug V, Diculescu M, Portincasa P, Dumitrascu DL. Small intestinal bacterial overgrowth is associated to symptoms in irritable bowel syndrome. Evidence from a multicentre study in Romania. Rom J Intern Med. 2014;52(3):143-50.

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