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Low FODMAP Diet for SIBO: A Step-By-Step Guide

Written by Dr. Michael Ruscio, DC on December 30, 2024

Written by Dr. Michael Ruscio, DC on December 30, 2024 — Reviewed by Hannah Wright

• A Low FODMAP Diet for SIBO: Yes or No?|
• Low FODMAP Diet for SIBO: Your Guide|
• Additional SIBO Solutions|

Small intestinal bacterial overgrowth, or SIBO, is just what it sounds like, too much bacteria in your small intestine. The digestive symptoms of SIBO include abdominal pain, bloating, and gas, but it can also cause brain fog and joint pain. In other words, it’s no fun and can be quite distressing.

So, if you’re struggling with SIBO, you’re probably on board with trying just about anything to get rid of it. Fortunately, there’s no need to go to extremes. We have a very effective, natural, research-backed option—a low-FODMAP diet.

In this article, I want to share with you why a low FODMAP diet is so effective for SIBO and clear up the confusion about conflicting advice you may hear. I’ll also provide a step-by-step guide for using a low FODMAP diet for SIBO and offer guidance on the next steps if it doesn’t completely resolve your symptoms.

A Low FODMAP Diet for SIBO: Yes or No?

A resounding YES—a low FODMAP diet is a great option for treating SIBO! Let me get into the details of why you don’t want to overlook this impactful therapy. 

A low FODMAP diet (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) restricts the amount of fuel (fermentable carbohydrates and prebiotics) for your gut bacteria. With less fuel, they die off or move back down into the lower GI tract (large intestine), where they should naturally be. We have a lot of evidence for using a low FODMAP diet for irritable bowel syndrome (IBS) 1 2 3 4 5 6 7 8, but the science is growing for this type of dietary change in SIBO too:

• A randomized controlled trial (RCT) found a low FODMAP diet reduced SIBO infections and symptoms after just 2 weeks 9.
• A clinical trial found a 6-week low FODMAP diet effectively resolved symptoms in 66% of patients with IBS and inflammatory bowel disease (IBD) with or without SIBO 10.

Reducing bacterial fuel explains some of the symptom-improving benefits of a low FODMAP diet for SIBO. But that’s not the end of the story—we have many very important research studies demonstrating the healing ability of a low FODMAP diet for your digestive system as well.

SIBO can increase inflammation, induce leaky gut, and trigger your immune system—research confirms a low FODMAP diet addresses all of these 11 12 13 14. But this dietary pattern also reduces histamine 15 16 and increases the density of enteroendocrine cells (cells in the gastrointestinal tract that regulate motility, secretion, absorption, circulation, local immune defense, cell proliferation, and food intake) 17. 

One of the criticisms of a low FODMAP diet is its potential to disrupt the gut microbiome. While this may have been a valid concern several years ago, we have research now that provides more clarity. Let me spend some time unpacking this and helping you understand how to avoid any adverse gut microbiome effects. 

Does a Low FODMAP Diet Harm the Gut Microbiome?

It’s still common to hear people claim that a low FODMAP diet does more harm than good. Since it limits fermentable fibers and variety, this type of meal plan may hypothetically impact the gut microbiome, especially if used long-term. Luckily, recent scientific evidence has given us some more insight. 

A 2023 literature review of 14 studies looking at patients with IBS who followed a long-term (6 months or longer) low FODMAP diet concluded that the diet can be safe and sustainable for up to one year without compromising nutritional intake, weight, body composition, or the gut microbiome, given it’s done correctly 18.

Additionally, a low FODMAP diet may even improve nutrient status in some people. SIBO and other digestive conditions can reduce your ability to absorb nutrients. Corrective and reparative therapies, like a low FODMAP diet, can target the root causes of nutrient malabsorption to improve nutritional status. 

A 2021 clinical trial of 36 IBS-D patients who followed a low FODMAP diet for 3 months found the low FODMAP diet improved leaky gut markers (zonulin, lipopolysaccharide, and lactose/mannitol ratio). But it also improved vitamin D levels by 11% in patients with sufficient levels and 80% in patients with a vitamin D deficiency (<20ng/dL). The researchers felt these benefits could have been due to the diet itself or better intestinal health overall 19.

Hopefully, this has eased any fears about a well-planned low FODMAP diet. When it comes to maintaining gut microbiome balance and nutritional adequacy while you’re on a low FODMAP diet (or any elimination diet, for that matter), it’s important to consume a wide variety of foods. For optimal results, it’s best to work with a registered dietitian or certified nutritionist who can correctly guide you through the process. 

Alright, now that you know a low FODMAP diet is a great option for SIBO, let’s get into the meat and potatoes of how to implement it successfully.

Low FODMAP Diet for SIBO: Your Guide

A low FODMAP diet has three phases: an elimination phase, a reintroduction phase, and a personalization phase. Before we get into the specifics, I want to stress the importance of working with a qualified healthcare professional when implementing a low FODMAP diet.

Elimination Phase

During the elimination phase (about 4–6 weeks, but could be up to 3 months), it’s easy to assume that you need to aim for zero FODMAPs in your diet. But as with so many things in life, the dose is the poison. Here’s an analogy to consider—if you’re exercising too much and you need some time to recover, this doesn’t mean you don’t exercise at all. Instead, you reduce your exercise load to an amount that allows your body to balance and heal. So when you’re in the elimination phase of a low FODMAP diet, rather than thinking you need to completely eliminate all FODMAPs, think in terms of reducing the load to an amount that will help you achieve gut microbiome balance.  

Monash University has some excellent resources that make implementing this type of diet much less daunting. For example, their low FODMAP diet app can help you navigate the various low FODMAP diet stages more easily. And just like I mentioned earlier, the app helps you understand why the amount of the food is so important. I’ll use broccoli as an example—broccoli isn’t typically allowed on a general low-FODMAP diet that you find online, but the app shows you that you can eat 2.65 ounces of broccoli (almost 1 cup) before getting into higher-FODMAP territory. The gist here is that you don’t have to completely delete broccoli and many other nutritious foods from your diet to see benefits. 

Here’s a snapshot of a low FODMAP diet:

If a low FODMAP diet is the right option for you, you should notice improvements in 2–3 weeks. I’m not saying you’ll be 100% better but many of our clients in the clinic seem to experience symptom improvement in this timeframe. Keep in mind, it could take 2–3 months to notice peak improvement. 

An additional consideration when following a low FODMAP diet for SIBO is the addition of probiotics. Why do we want to add probiotics (bacteria and fungi) to your gut if it’s overrun with bacteria (and possibly fungi)? It turns out that probiotics can produce a number of antimicrobial compounds that allow them to poke holes in microbial cell walls, inhibit their cell metabolism, prevent them from sticking to your GI mucosa, increase their oxidative stress, and flat-out kill them 20. 

We have strong research showing probiotics alone can eradicate SIBO and its related symptoms:

• A meta-analysis found probiotics alone eradicated SIBO in 53% of patients 21
• A clinical trial found probiotics worked better for GI symptoms when patients had SIBO 22

This is excellent news, but it gets even better! A recent randomized control trial found that adding probiotic supplements to a low FODMAP diet reduced SIBO infections and symptoms even more than just the diet alone 9.

This data is really compelling and mirrors what we’ve seen in the clinic with our triple therapy probiotic approach for SIBO.

Once you’ve gone through 4–6 weeks of eliminating high FODMAP foods, it may be time to start the reintroduction phase. Let’s discuss how to know when to start adding foods back in.

Reintroduction

When it comes to reintroducing eliminated foods, I’ve noticed my clients tend to fall into one of two camps—either they’re hesitant to add anything back for fear of feeling bad again, or they’re ready to add  everything back at once because they feel so great. Both of these situations can set you up for failure. Let me explain. 

If you’re resisting the reintroduction, you may not be getting the nutrients you need depending on how restrictive the diet is. It’s likely safe to follow a varied low FODMAP diet for even up to a year, but if the diet is too restrictive, you could run into some issues like nutrient deficiency, weight loss, or gut microbiome imbalances 18. Additionally, you may suffer psychologically from feeling deprived or unable to participate in social situations that involve food. 

On the flip side, rushing the reintroduction can make it difficult to discern food intolerances or which foods may be trigger foods for you. In my experience in the clinic, a balanced approach to food reintroduction is crucial for long-term success.

Unfortunately, knowing when to start the reintroduction isn’t an exact science. An observational study of patients with GI conditions who followed a low FODMAP diet found they tended to do better when they waited 1–2 months before trying high FODMAP foods 23. So, if you’ve been on a low FODMAP diet for 4–6 weeks, use your symptoms as a guide for moving forward: 

• If your symptoms have dramatically improved, then you may want to start reintroducing eliminated foods.
• If your symptoms are only somewhat improved, then you may want to stick with the elimination phase for several more weeks.
• If your symptoms haven’t improved much at all, then it’s time to consider other therapies like herbal antimicrobials or an elemental diet—I’ll get into this in more detail later.

It’s best to work with a trusted healthcare provider, like a dietitian, to help you on the reintroduction journey. But generally, you’ll utilize a structured reintroduction approach where you test one food from each FODMAP subgroup at a time (in the context of eating low FODMAP foods as your baseline), allowing 3 days per food for sensitivity reactions or signs of intolerance to arise 24. 

Here’s a table of each FODMAP subgroup and sample challenge foods:

When you’re ready to start reintroducing foods, keep a food diary or spreadsheet (or use an app) to track symptoms like diarrhea, constipation, bloating, gas, and reflux. Don’t forget non-digestive symptoms like rashes, hives, joint pain, brain fog, fatigue, headaches, and anxiety. When you hit the personalization phase, you’ll be glad you kept track of this information.

Here’s one way to go about reintroducing foods:

• On day 1, have a small amount of milk at a meal (while still following a baseline low FODMAP diet), and observe for any adverse symptoms over the next day or so.
• If you don’t have any symptoms, then have a larger serving of milk, possibly at each meal, on days 2 and 3 to determine how much you can tolerate before having symptoms.
• If you do have significant symptoms, then remove milk from your diet again and go back to your baseline low FODMAP diet for a couple of days before moving on to the next new food.
• After a couple of days, move on to the next FODMAP subgroup and repeat the process.

As you go through this process, you can also challenge different foods that are in the same FODMAP subgroup. For example, if you’re reintroducing fructans, you may want to try three different fruits that are high in fructose during your three-day trial—an apple on day one, blackberries on day two, and green grapes on day three. Using this method may give you more insight into specific food triggers and move the process along more quickly.

It may seem complicated, but this structure allows you to better understand your FODMAP triggers and alleviate FODMAP food fear. It’s always best to listen to your body and go at your own pace. It’s probably not the best idea to start food reintroductions on bad gut days—and we all have times when our gut just feels off. So, starting on a day when you’re feeling great gut-wise, calm, and positive can go a long way when it comes to your results. 

Now, it’s time to personalize your maintenance meal plan using the information you gleaned from the reintroduction. 

Personalization

A low FODMAP diet isn’t meant to be a long-term meal plan. Rather, it’s an investigative tool we use short-term to learn about your FODMAP tolerance 25. The overall goal is always to have the most varied diet possible.

When it comes to personalizing your long-term meal plan, you’ll want to keep in well-tolerated foods and avoid or limit the amounts of foods that don’t sit well with you—this is where your symptom journal will come in handy.

Be mindful that some foods may not work for you now, but as your gut microbiome becomes more balanced and your gut health improves, it’s entirely possible for you to tolerate those foods later on. So, if you have any FODMAP foods you continue to restrict in your maintenance meal plan, I encourage you to go through challenge periods off and on to see if and when you can add any of those foods back. 

A low FODMAP diet for SIBO, along with probiotics, can be very effective. But what do you do if it doesn’t work for you? Fortunately, we have other options.

Additional SIBO Solutions

It can be pretty disheartening to follow a special diet and take probiotics for weeks and not get the results you’re hoping for. Thankfully, there are other effective SIBO treatments like herbal antimicrobials or antibiotics, and an elemental diet to help you find relief. 

Antibiotics and Herbal Antimicrobials for SIBO

If you’ve been pretty consistent with a low FODMAP diet and probiotics but still feel unwell, it may be time to discuss other options with your healthcare provider. Antibiotics, like rifaximin (Xifaxan), may eradicate SIBO in 50–60% of patients 26 27, and when combined with probiotics, the eradication rate improves to about 86% 21. However, rifaximin isn’t always covered by insurance and can come with a hefty price tag. Plus, you may feel more comfortable with a more natural solution, which is where herbal antimicrobials come in.

Herbal antimicrobials, like oil of oregano, berberine 28 29, and sweet wormwood 30 31, are plant and herbal extracts that knock out offending microbes. I don’t use herbal antimicrobials as a first-line option, but they’re helpful for getting you over the finish line when you need it. Herbal antimicrobials don’t require a prescription and they work at least as well as rifaximin 32. And herbals have other benefits like lowering inflammation and fighting fungi and parasites, whereas antibiotics only work against bacteria 29 33 34 35 36. One drawback with herbal antimicrobials may be that they take longer to work, about a minimum of 1 month 32.

Our team conducted a small clinical trial using herbal antimicrobials, with or without enzymes that dissolve biofilms. We found our herbal preparation eradicated SIBO in about 40% of clients, which is similar to what research has found with antibiotics. 

Here’s a side-by-side comparison of herbal antimicrobials v/s antibiotics for SIBO:

To sum this up, both herbal antimicrobials and antibiotics, especially when combined with probiotics, can be very effective for SIBO. It’s best to work with a healthcare professional when using either of these. You can find more information about the protocol we use in the clinic in my book, Healthy Gut, Healthy You.

Now let me share another natural treatment solution for SIBO—an elemental diet.

Elemental Diet for SIBO

An elemental diet is a liquid meal replacement shake that gives your digestive system a chance to rest, heal, and then repair 37 38. This therapy also reduces inflammation 37 39 and starves SIBO and other bacterial overgrowths 40.

Unfortunately, we don’t have much scientific evidence on the use of elemental diets for SIBO. The highest quality research is from a 2006 clinical study that showed a 2-week elemental diet may have cleared SIBO more effectively than antibiotics 40. But not having much research doesn’t necessarily mean an elemental diet isn’t a valid therapy—I’ve used elemental diets successfully with clients who have many different GI conditions in the clinic.

I don’t recommend an elemental diet as a first-line treatment. But if you’ve given diet, probiotics, and either herbal antimicrobials or antibiotics a chance and need an additional boost, it can be a great option. In the clinic, I most often use an exclusively elemental diet as a 2–4 day gut reset. However, there are many ways to incorporate this therapy into your plan, so I encourage you to work with a qualified healthcare professional to determine what’s best for you. 

Heal SIBO Symptoms with a Low FODMAP Diet

SIBO can cause digestive distress and other symptoms outside the gut, like fatigue and brain fog. Fortunately, you don’t have to go to extreme measures to recover great gut health. Research supports the use of even a long-term, well-planned low FODMAP diet for SIBO and suggests that adding probiotics to the diet can enhance your results. 

A low FODMAP diet has three phases: elimination, reintroduction, and personalization. Ideally, you’ll work with a trained healthcare professional when implementing this process to help you achieve maximum results and avoid any negative consequences.

If you follow the low FODMAP diet and use probiotics for 4–6 weeks but your symptoms don’t seem to be significantly improved, you may want to speak with your healthcare provider about herbal antimicrobials or antibiotics and an elemental diet. My book Healthy Gut, Healthy You also walks you through a step-by-step gut-healing guide, and we offer one-on-one consultations at the Ruscio Institute for Functional Health. 

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