The Low FODMAP and other low fermentable fiber diets are often considered the go to approaches for SIBO and IBS sufferers. The theory behind the low FODMAP diet is to reduce fermentable fibers that gut bacteria can eat. High FODMAP foods are fermented in the gut and this breakdown of fiber can cause increases in gas production that can lead to symptoms seen in IBS and SIBO.

But while these diets may help reduce symptoms at first, they should not be viewed as a long term dietary solution for gut problems.

Through my experience working with clients, I tend to see a worsening of gut issues from long term dietary fiber or FODMAP restriction. Usually, individuals who have been low FODMAP for a long time also become more intolerant to fibers over time as their microbial community loses diversity and abundance of microbes important for fiber breakdown. Not to mention the mental and physical stress of trying to maintain a low FODMAP diet.

I wanted to touch back on this topic as 2 new studies have been released and provide some additional evidence that conflict with the idea that low fermentable fiber diets are best for those with functional GI disorders like IBS and SIBO. Let’s dive in.


Effects of Prebiotics vs a Diet Low in FODMAPs in Patients with Functional Gut Disorders.

This study was meant to compare the low FODMAP diet head to head against prebiotics. You might be thinking- if prebiotics feed gut bacteria, wouldn’t they make symptoms worse for someone with IBS or SIBO? On the surface prebiotics may sound like a bad idea for someone with gut issues like SIBO, but both IBS and SIBO studies where prebiotics were used as an intervention for gut symptoms have shown positive outcomes.

Both Low FODMAP an prebiotics have shown positive outcomes, but they are polar opposite approaches.

I wrote extensively about this in my prebiotic article that you can check out here. But, the gist from these past studies on how prebiotics help IBS and SIBO patients is due to the prebiotics ability to increase Bifidobacterium levels in the gut. These bacteria are crucial for maintaining your gut barrier, reducing inflammation in the gut and promoting MMC activity. Low FODMAP has been shown to reduce levels of this bacteria, which could be problematic to the long term health of your gut.

In this particular study, the researchers wanted to get a better understanding of how these two opposite approaches improve symptoms and also if one was superior to the other. The primary outcome they wanted to look at was microbial composition changes in the stool. Secondary outcomes were digestive sensations and intestinal gas production.

The study was a randomized controlled trial of individuals with functional gut disorders (which includes SIBO and IBS) that have GI symptoms with flatulence. The participants were separated into 2 groups: a prebiotic group and a Low FODMAP group.

The prebiotic group consisted of 19 people who were all put on a Mediterranean diet and 2.8 g/day of Bimuno (beta-GOS prebiotic supplement). I am familiar with Bimuno and have used it successfully with clients, so I was happy to see it being used in the study.

The Low FODMAP group consisted of 21 people and they ate low FODMAP and took a placebo pill instead of the prebiotic. The prebiotic and Low FODMAP intervention were done for a 4 week period and then the participants were followed for an additional 2 weeks after they ended the intervention.

As suspected, Bififobacterium increased in the prebiotic group and decreased in the Low FODMAP group. But, the most interesting shift in the gut bacteria was how these two interventions shifted a bacteria called Bilophila wadsworthia. The low FODMAP diet group had increased levels of this bacteria and the prebiotic group had decreased levels of these bacteria.

Bilophila wadsworthia is a gram negative organism that is a normal resident of the gut flora, but high levels of this bacteria has been linked to gut barrier breakdown and systemic inflammation. The low FODMAP diet increased levels of this bacteria while the prebiotic intervention reduced levels of these bacteria. I hypothesize that the elimination in fermentable fibers leads to an intestinal environment where this bug can start to overgrow, while a diet that includes fibers can help keep bilophilia wadsworthia in check.

B. wadsworthia is also a hydrogen sulfide producer and could play a role in the hydrogen sulfide form of SIBO. Therefore, I hypothesize that a low FODMAP could predispose you to developing a hydrogen sulfide overgrowth. 

But, how did each of these groups feel during the intervention? Both groups had significant reductions in all symptom scores, except for flatulence and gurgling/rumbling sounds. It makes sense that the prebiotic group still had gas and rumbling because fibers are fermented to produce gas. You don’t want to eliminate all gas or rumbling in your stomach. The healthy level of gas and rumbling is just a sign that your gut bugs are doing their job!

The researchers also followed both groups for 2 weeks after the intervention. The Low FODMAP group’s symptoms came back right when they stopped the Low FODMAP diet. The prebiotic group’s symptom relief persisted for the 2 weeks that the researchers followed them after the experiment.

The researchers concluded that while both interventions reduced symptoms, prebiotic supplementation may be a more viable long-term alternative to dietary restriction for people with functional gastrointestinal disorders.

The one criticism that I have with the study is that the prebiotic group was on a Mediterranean style diet that could have also added to the benefits seen in the prebiotic group. The Mediterranean diet is rich in polyphenols and other antioxidants that can increase the growth of good gut bugs and lower inflammation.

The big takeaway is that if you have SIBO or IBS, you may benefit from including prebiotics in your diet and through supplementation. You should not live in fear of FODMAPs or prebiotics.

Study #2:

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

This study included 126 patients with GI symptoms and 38 healthy volunteers who were tested for SIBO through an endoscopy and a duodenal aspirate. In this study, they wanted to see if GI symptoms correlated with SIBO and an altered small intestine microbiome. They also did a pilot intervention where they analyzed the effect of diet change on gut symptoms by putting 16 healthy higher fiber eaters on a low fiber, high simple sugar diet for 7 days.

This study is so so so fascinating and could change how we view SIBO for two really big reasons. First, it found that GI symptoms did not correlate with a positive SIBO test through a duodenal aspirate, which is considered the gold standard of SIBO testing. Simply put, many symptomatic patients did not test positive for SIBO while healthy controls did test positive for SIBO.

While GI symptoms were not correlated to a positive SIBO test, symptoms DID correlate with an altered small intestinal microbiome. Those with GI symptoms, had a different microbial profile compared to healthy controls without GI symptoms. Symptomatic patients had significantly lower microbial diversity, richness and evenness. Levels of Porphyromonas, Prevotella, and Fusobacterium bacteria were significantly lower in symptomatic patients.

A subset of the symptomatic patients (29%) were found to have significant small intestinal dysbiosis. SIBO was not associated with small intestinal dysbiosis either!

The researchers also isolated factors that differentiated healthy controls from these symptomatic patients. They found that advanced age, PPI use, recent antibiotic use and past GI surgery were all factors that differentiated symptomatic patients from healthy controls.

In addition, the bacterial composition in symptomatic patients versus healthy controls supported different metabolic pathways. Symptomatic patient’s bacteria were associated with simple sugar breakdown while healthy controls bacteria were associated with complex carb breakdown. These different bacterial profiles suggested that symptomatic patients may be eating more simple sugars causing a shift in bacteria.

The bacterial compositions alone was not enough evidence to conclude that a diet high in simple sugars leads to changes in the small intestine microbiome that lead to GI symptoms. The researchers decided to do a pilot study to help them explore this hypothesis further.

They used 16 healthy controls who were eating a higher fiber diets and put them on a diet low in fiber and high in simple sugars for 7 days. Interestingly enough, 8 out of the 16 healthy controls without GI symptoms actually tested positive for SIBO. Researchers speculated that SIBO may be a result of their dietary preference towards fiber.

Before the study, the average fiber intake was about 25 grams per day. During the study, the average fiber intake dropped to about 9 grams per day. The patients were eating over 50% of their carbohydrates from simple sugar sources.

I couldn’t find info on what type of simple sugars were used in the study. Simple sugars could mean added sugar or it could mean fruit. It would have been nice to get a breakdown of what constituted the the simple sugars that were being consumed.

ALL 16 patients developed new symptoms on the low fiber diet with 80% developing GI symptoms during the dietary intervention. The symptoms resolved within a week of discontinuing the diet.

The shift in diet led to lower diversity of bacteria in the gut and more small intestinal permeability (leaky gut). Lower diversity was also associated with post meal bloating and abdominal discomfort that was relieved by having a bowel movement.

The researchers found acetate and butyrate to be reduced with the low fiber, high simple-sugar diet. As stated in the paper “these microbial fermentation products are a key energy source for intestinal epithelial cells and play an important role in epithelial barrier integrity and enteropathogen exclusion.”

So, what are the key takeaways from this study?

First, it shows that we may need to focus more on the microbial composition of the small intestines versus the excess of bacteria in the small intestines since healthy controls tested positive for SIBO by the gold standard duodenal aspirate measurement. Cyclical antibiotic and herbal strategies typically used to treat SIBO may further small intestinal dysbiosis and make matters worse in the long run.

Just to be clear, I am not saying that all clearing or pruning strategies are bad. In fact, some clearing with herbals or even antibiotics may be helpful, but it is easy to go overboard with these strategies if you are using these approaches chronically to control symptoms without addressing root causes.  

To compound the problem of overkilling, you may be on a restrictive diet that reduces fibers. You might even fear fiber (I know I was guilty of this when I had SIBO). Jumping on a long term low FODMAP diet is all the rage in the SIBO/IBS world, but this could further deplete bacterial diversity in the small intestines leading to symptoms as seen in the healthy controls that shifted from a high to low fiber diet.

This study provides further evidence that by limiting fiber, as most SIBO diets do, we may be creating more imbalance, permeability and inflammation in the small intestines. A diet diverse in fibers appears to play a key role in promoting barrier function and diversity of microbes in the small intestines.

While this study does have its limitations being that it was a small pilot study, I am excited to see future studies that start expanding our understanding of the small intestine microbiome and how we can best facilitate change through dietary interventions.

Both of these studies support what I have seen working with many SIBO clients. Restricting does not help long term. Those who have been on strict SIBO diets long term are usually worse than those who have made less extreme dietary changes. It also becomes much harder to reincorporate fibers back into the diet when you have restricted.

I have also had success in many cases using prebiotics with clients. A prebiotic approach to feed gut bugs is a polar opposite than a SIBO diet that attempts to starve gut bugs. Prebiotics are a totally underutilized tool in the SIBO/IBS world.

Bottom Line:

SIBO diets might be all the rage, but they will fall short to provide long term relief. Focusing on strategies that rebalance the small intestines microbes may be a superior long term strategy than trying to starve your gut bacteria of fermentable fibers.

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  • So…can you help us out with what we should be eating if we’re doing okay on the low fodmap diet (for 3 weeks after Xifaxin)? Move on to Mediterranean? Move on to higher fodmaps? Etc…..
    Thank you!

    • Hi Kathy! I would reintroduce more fermentable fibers like FODMAPs that you have cut out. Start low and slow for sure, but you can move at your own pace.

      • When introducing simple prebiotics back in (acacia, inulin, etc.) I eventually get GERD. How does one introduce prebiotics/fiber without adding to the problem?

      • Hi Guinevere, great question. The type of prebiotic fiber can make a big difference in how you will respond. I find that inulin is usually not as well tolerated as GOS. Sometimes people do better with PHGG as well. It just really depends on the person. Also building up the dose slowly can be helpful. Understanding the root cause of your GERD is also important. Treating any infections like h. pylori and even lingering SIBO imbalances can be important in order to tolerate more foods. I hope his helps 🙂

    • Hi Marcela, I am slightly confused about what you are asking. Can you clarify for me? Thanks!