Special Report: 8 Pitfalls of the Low FODMAP Diet For IBS and SIBO

Plus tips to help you determine what diet is right for YOU

The Low FODMAP diet is a popular diet for IBS and SIBO. FODMAP stands for "Fermentable Oligosaccharides, Disaccharides, Monosaccharides And Polyols. The key word in this definition is “fermentable”. Microbes are fueled by the fermentation of FODMAPs. In simple terms, FODMAPs are food for your gut bugs.

In a dysfunctional or imbalanced gut, these FODMAPS can result in bloating, gassiness, discomfort and diarrhea/constipation. The philosophy of the low FODMAP diet is to remove the fermentable fibers to starve the gut bugs. With less fermentation in the gut, you may notice short term GI symptom relief.

While the diet may reduce symptoms, it is a band aid solution. It does not correct any of the dysfunction that caused reactions to FODMAPs in the first place. A balanced and functional gut will not react to FODMAPs. In fact, FODMAPs may be needed to keep the gut healthy.

In this article, I want to highlight the 8 biggest pitfalls of the Low FODMAP diet. I have experienced each of these pitfalls personally when I went on the Low FODMAP diet for 4 months. In addition, as a dietitian that specializes in gut health, I work with many SIBO/IBS sufferers who have dug themselves into a deeper hole by following the low FODMAP diet. 

1. The Low FODMAP Diet is not a long term solution.

The Low FODMAP diet was designed for short term use for about 6-8 weeks followed by a reintroduction period. Doing a short term low FODMAP may be helpful for some people. I am not anti-FODMAP when it is used in this manner. 

However, most of the SIBO sufferers I have talked to will go on this diet for months, years or forever. While there are many short term studies that show symptom reduction on Low FODMAP, there are no studies (that I am aware of) that show staying on a stict Low FODMAP diet yields the beneficial outcomes longterm.

Through my experience working with hundreds of SIBO/IBS clients, I find that restricting FODMAPs long term usually yields poor results. Not only does long term low FODMAP not work, it can sometime lead to additional problems like weight loss, nutrient deficiencies, further gut imbalances and more (all of which I will cover in more detail as I continue in with this article)

If you want to try Low FODMAP, I have found it tends to be most successful when you use it as designed for short term symptom relief for 4-8 weeks. I would also work with a registered dietitian who can help guide you through the diet and the reintroduction phase.

2. The Low FODMAP diet does not address root causes of gut dysfunction

If you take nothing else away from this article, take this: the low FODMAP diet does not correct problems that underlie gut symptoms. You have GI issues because your gut is imbalanced and/or your digestive function is impaired.

The Low FODMAP may starve an imbalanced gut which yields less gas production and symptoms. But, the dysfunction and imbalances that caused the symptoms in the first place are still present. As I mentioned earlier, it is a band aid solution.

For long term relief from gut issues, you must address the root cause of your gut issues. Some of the major root causes I see in my clients are brain-gut axis dysfunction, gut dysbiosis (imbalances), cortisol dysregulation, low stomach acid, liver/bile flow problems and thyroid dysfunction.

Not only does the low FODMAP fail to address root causes, but long term adherence can worsen root causal issues.

3. The Low FODMAP diet has been shown to lower levels of good gut bugs

One of the big reasons why I hypothesize that low FODMAP isn’t beneficial for many is because it's been shown to deplete Bifidobacterium levels. A healthy level of Bifidobacterium is essential for a healthy gut.

Bifidobacteria have been shown to increase transit time, promote short chain fatty acid production, protect the gut lining, increase immunity, prevent GI infections and even help in the production of bile acids. 

Interestingly enough, one study found that people with IBS had a 2-fold reduction in bifidobacteria compared to healthy controls. This leads me to wonder….if low bifidobacteria is associated with gut dysfunction, should a diet that further reduces these good bugs be the go to diet for IBS and SIBO?

I would hypothesize that the low levels of Bifidobacteria may be a root causal factor driving the gut symptoms associated with IBS. When we feed our good bacteria, they produce short chain fatty acids like butyrate, acetate and propionate. Butyrate is the preferred fuel for the cells lining the GI tract and increases immune function in the GI tract. Acetate and proprionate improve motility and reduce inflammation. Low levels of these acids are associated with leaky gut, autoimmunity and systemic inflammation.

Jeff Leach, a researcher involved in the Human Microbiome Project, points out that these acids are key to providing the optimal pH in the gut to promote the growth of good bacteria like Bifidobacteria and to prevent the growth of pathogenic bacteria. He explains that “many pathogenic bacteria are pH sensitive” and when we reduce fermentable fibers our colon becomes less acidic. He explains that this unfavorable shift is like “opening pathogen’s door.”

Another huge problem with the Low FODMAP diet is that it limits diversity in the diet which hinders diversity in your gut. An ecosystem operates best if there is a diverse population of organisms that each fulfill a specific task. The same phenomenon happens in the gut.

Microbes in the gut perform tasks for us that you can not perform on your own. Different microbes perform different important tasks. To give you a few examples, certain microbes make vitamins for you while others help metabolize your hormones. Diversity also helps keep microbes balanced and prevents overgrowths. The more diverse the microbiome the better!

Diversity in the gut is created by diversity on the plate. Every gut bug has their favorite food. If you narrow the diversity of your diet, you won’t be feeding as many gut bugs. By cutting out foods from your diet, you could be reducing the diversity of the gut bacteria even further.

By reducing fermentable fibers on a long term Low FODMAP diet, you run the risk of creating a gut environment that favors pathogens versus good gut bacteria. If you struggle with IBS or SIBO, you can’t just focus on starving the gut, but eventually you need to focus on rebalancing/rebuilding healthy populations of good gut bugs. It is virtually impossible to do that on a strict Low FODMAP diet.

4. The Low FODMAP diet can lead to nutrient deficiencies that can negatively effect gut and overall health

The more restrictive your diet is, the higher the risk of developing nutrient deficiencies. This risk is especially high if you are doing the diet on your own without close supervision of a dietitian or other practitioner. Nutrient deficiencies can affect virtually every aspect of your health. And when you are battling SIBO/IBS, nutrient deficiencies become even more problematic.

In a recent webinar, Kiran Krishnan, a Microbiologist specializing in the microbiome, discussed how restrictive diets can disrupt the healthy function of the immune system in the gut by reducing the secretory IgA in the gut mucosa. Secretory IgA is an antibody found in the mucous layer above the gut lining that serves as the first line of defense in protecting us from toxins and pathogenic microorganisms that we consume.

It is important to remember that food, bacteria and toxins have to be absorbed through the gut lining to truly enter the body. IgA neutralizes any threats in the mucous on top of the gut lining and prevents entry into the body.

In terms of SIBO, IgA is essential for fighting off and preventing overgrowths of bacteria in the small intestine. When IgA becomes low, bacteria, toxins and food will bypass the mucosa causing an immune response which creates an inflammatory cascade in the body.

The immune cells in the gut lining essentially think they are under attack and this chronic over stimulation of your immune system can lead to both immune and gut barrier dysfunction. So, when levels of IgA are low, your immune system won’t be able to remove unwanted pathogens and your gut will be inflamed preventing SIBO recovery.

Krishnan says that when individuals with gut issues and food sensitivities limit the diversity of their diet, their secretory IgA usually declines. He attributes this mostly to nutrient deficiencies that ensue from a restricted diet. Zinc, vitamin C, selenium, choline, glutamine, glycine and omega 3 fatty acids are key nutrients for IgA formation. Eating a wider variety of foods makes it much easier to achieve adequate levels of these nutrients.

Nutrient deficiencies don’t just effect IgA levels. Nutrient deficiencies can lead to many systemic symptoms like fatigue, poor immunity, headaches, decline in skin/hair/nail health, depression, brain fog and more! Many restrictive dieters come to me for help with systemic symptoms from only eating a handful of foods. It is very hard to meet nutrient needs on a very restrictive diet. 

5. On the low FODMAP diet, you starve your gut bugs and they could start eating you

In an interview, Stanford microbiome researcher, Dr. Justin Sonnenburg, stated “when you starve these microbes they start eating you. When you don’t eat dietary fiber, you are forcing the microbes into a position where they are forced to consume the important immunological barrier in your gut.”

The important immunological barrier that Dr. Sonnenburg is referring to is the gut lining. Above this gut lining, is a mucous layer that serves as a protective buffer preventing direct contact of the epithelial lining from bacteria and toxins.

My beautiful gut lining masterpiece

This mucosa also serves as a habitat and food source for our colonic bacteria. When your mucous layer is thin, bacteria and toxins will come into contact with the epithelial lining and elicit the same inflammatory immune response that occurs from low IgA.

The goblet cells within the gut lining produce mucins, which are the building blocks of the mucous layer. The primary fuel source for these goblet cells are the short chain fatty acids that are the product of intestinal bacteria fermenting carbohydrates like FODMAPs. So, when you don’t eat fermentable carbs, your goblet cells can’t produce enough mucous.

Without fermentable fuel and adequate mucous, the bacteria become ravenous, eating through all the mucosa and they will eventually start consuming your gut lining. This degradation of the gut barrier will not only lead to gut dysfunction, but system wide inflammation.

SIBO suffers, myself included, are guilty of demonizing FODMAPs to such an extent that we lose sight of how important FODMAPs and fermentable fibers are to the overall health of our digestive system. We must not fear fermentable carbs. FODMAPs help keep a mucous rich digestive tract ensuring a strong gut barrier.

6. Low FODMAP diets can lead to undereating and weight loss

Working one-on-one with many gut clients has totally opened my eyes to the undereating problem in the gut health space. Any time you are cutting out a large amount of food from your diet, you can run the risk of undereating and losing weight. 80% of the clients I work with were undereating before we started working together. Therefore, it is not surprising that many are struggling with unintentional weight loss when they under eat on restrictive diets. 

I personally lost weight during my own gut healing journey following a strict Low FODMAP and SCD diet. I dropped about 15-20 lbs in a few months and I was already thin to begin with. I felt horrible. 

Meeting calorie needs on a Low FODMAP diet is not impossible, but I rarely see people succeeding to meet their needs on this diet. Based on my work with clients, it seems that many practitioners over emphasize what foods should and should not be eaten and fail to ensure that their patients are well nourished.

You cannot heal your gut if you are not nourished. Meeting your calorie needs should always be number 1 priority before deciding what foods you should or should not be eating.

Undereating can actually lead to more gut symptoms. If you are malnourished, you will activate your HPA axis leading to a rise in the stress hormone, cortisol. Elevated cortisol levels derail digestion by reducing blood flow, enzymatic release and nutrients to the gut, which impair digestion and weakening gut barrier function. Therefore, chronic stress activation from malnutrition creates a dysfunctional gut that is susceptible to imbalances and overgrowths. 

This diagram below depicts how undereating leads to gut dysfunction. 

HPA axis activation will also down regulate thyroid hormones to slow down metabolism to better preserve limited calorie intake. Low thyroid hormones slow gut motility and results in constipation. This gut slow down also lead to an environment ripe for microbial overgrowths like SIBO.

To make matters worse, undereating and weight loss is often not taken seriously. But, weight loss should not be dismissed. If you are losing weight, you should work with a  dietitian to reverse weight loss. You also should consider broadening up the diet so that you can better meet nutrient needs. 

7. The Low FODMAP diet is a recipe for food fears and stress

When I was on the Low FODMAP diet, I was irrationally terrified of high FODMAP foods. I felt like I was always walking on thin ice and if I had one too many Brussel sprouts that I was going to crash through that ice. My mind never had a break from planning out my meals and snacks. My will power was tested on a daily basis to stay Low FODMAP at all costs. Each day was a struggle and I felt like I didn’t have enough gas left in the tank to enjoy the activities that I usually loved doing.

Through my work with clients, I see the low FODMAP diet consistently driving food fears and stress. The low FODMAP diet is a recipe for disordered eating patterns to develop. The low FODMAP diet plants a seed in your head that foods are either good or bad. With that seed planted in your head, it can be very easy to start fearing foods. It can also make it much harder to reintroduce high FODMAP foods.

Your beliefs and perceptions of food play a major role in our biology. This phenomenon was described by Dr. Bruce Lipton in his book The Biology of Belief. Dr. Lipton writes, “Cells, tissues and organs do not question information sent to the nervous system. Rather, they respond with equal fervor to accurate life affirming perceptions and to self-destructive misperceptions. Consequently, the nature of our perceptions greatly influences the fate of our lives.”

To sum up this quote: If you believe you will react to negatively to a food, you will react negatively to that food. That is not to say that you can’t have true reactions to foods, but your beliefs/perceptions around food can blur your ability to pinpoint true reactions.

Dr Lipton writes “human beings have a great capacity for sticking to false beliefs with great passion and tenacity.” This quote sums up food fears perfectly. Similar to my own experience with food fears, many of my clients have experienced a worsening of symptoms and health overall on these diets. Yet, they still struggle to break free from them due to their false beliefs.

Another misconception that can drive destructive foods fears is that idea that you have to be low FODMAP to starve SIBO. You don’t develop SIBO because of a diet problem. Instead, you develop SIBO because of a breakdown in motility and digestive function. Therefore, you can’t truly starve the SIBO with a restrictive Low FODMAP diet. You have to address root causal breakdowns to heal from SIBO.

Food fears can keep you in a rut and prevent progress. Food fears can also prevent you from self-experimentation. Most gut health patients don’t need to avoid all the FODMAPs. Rather, experimenting helps you figure out which foods are your specific triggers. Once you have isolated your triggers, you can safely avoid your triggers without unnecessary restrictions.

8. Evidence that feeding gut bacteria increases the efficacy of SIBO treatments

Dr. Mark Pimental, a leader in SIBO research, has said that “happy and well-fed bacteria are more sensitive to antibiotics and easier to kill.” He recommends his patients eat plenty of fermentable foods during treatment to keep them active so that the antibiotics can effectively wipe out the overgrowth.

There is growing scientific evidence to support this feed to kill concept. A study found that eradication rates improved from 62% to 87% when Rifaximin was used in conjunction with a prebiotic (guar gum) compared to treatment with Rifaximin alone. The researchers concluded that “the prebiotic effect of PHGG (partially hydrogenated guar gum) is likely to provide a synergistic action with rifaximin inside the bowel lumen, by improving intestinal clearance and favouring the microflora balance.”

This evidence does not indicate that you need to force yourself to eat lots of FODMAPs that you don’t tolerate well. Instead, it suggests that eating some FODMAPs and other prebiotic fibers that you tolerate during treatment may help better treatment outcomes.

How to find YOUR diet Sweet Spot

Now that I have highlighted the issues with the low FODMAP diet, you may be wondering, what diet should I follow?

Let me state this clearly: there is not one right diet for SIBO. There is only the right diet for you! Instead of strictly following a list of yes and no foods, you must experiment to identify your specific triggers. You may be fine with most high FODMAP foods. You also may have low FODMAP triggers. But, it takes experimenting to find your sweet spot.

Your diet sweet spot is best depicted with this picture below. You want to find the point where you have eliminated triggers and inflammatory foods, but avoiding unnecessary food removal. I find that using a broad to narrow approach is the best approach when trying to pinpoint your diet sweet spot. Instead of the narrow to broad approach that is used with the Low FODMAP diet.

Please also note Step 1! Diet changes can help reduce symptoms, but root causal approaches are what can fix the underlying dysfunction. Diet change can only control symptoms so much. You must address root causes while you change the diet. You also want to make sure you are treating SIBO or gut infections/imbalances that could be driving the gut symptoms.

It can be easy to neglect other important aspects of treatment when you are spending all your time and energy restricting your diet. Diet should only be one part of your SIBO treatment. A multifaceted treatment approach is required to clear the overgrowth and address the root causes for you to make progress.

When I was on a super restrictive diet, I had no energy to address the stress, hormone issues, brain-gut axis problems and large intestine imbalances that were at the root of my SIBO. It was kind of like I was putting all my eggs in the SIBO diet basket. But when I only invested my energy and resources in perfecting my diet to treat SIBO, there was no payoff.

My payoff skyrocketed when I started to diversify my treatment strategy. Allowing some slack in my SIBO diet freed up energy and resources to address my root causes! My clients also make progress when they loosen the reigns on their diet to focus on other strategies like circadian rhythm repair, movement, stress management, vagus nerve support, detox support and rebuilding the gut (vs starving the gut). 

                                   Bottom Line

The Low FODMAP should not be the go to diet for IBS and SIBO. For some cases, it can be a helpful TEMPORARY tool to reduce symptoms, but I would try other strategies first. If you are doing low FODMAP or planning on trying it, I would try it under the guidance of a dietitian or knowledgable practitioner. 

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