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The Ultimate 3-Step SIBO Treatment Guide

Written by Dr. Michael Ruscio, DC on December 14, 2023

Written by Dr. Michael Ruscio, DC on December 14, 2023 — Reviewed by Dr. Hannah Hamlin

How to Use Science-Backed Therapies to Heal Your SIBO Symptoms Without Testing

• Overview|
• What You Need to Know|
• 3-Step Protocol|
• Step 1: Low-FODMAP Diet + Lifestyle|
• Step 2: Probiotics|
• Step 3: Antibiotics or Herbal Antimicrobials|
• Bonus: The Elemental Diet|
• SIBO Treatment Made Safe, Simple, and Effective|

It’s pretty common in the clinic to meet folks who have struggled for years with symptoms like brain fog, poor sleep, depression, skin issues, joint pain, and digestive symptoms. To find relief, most have tried numerous tests and supplements, with or without medications, but they have largely been unable to experience complete healing. 

If this sounds like you, you may want to consider small intestinal bacterial overgrowth, or SIBO, as a cause of your symptoms. SIBO isn’t a disease per se, but rather a condition in which you’ve got more gut bacteria in your small intestine than you should have. It’s pretty common, but fortunately, there are many safe, effective, science-based therapeutics, like diet, probiotics, and antimicrobials, to help you eradicate SIBO and restore healthy, robust gut function. So, let’s start off with an overview of the 3-step SIBO treatment protocol we use in the clinic.

SIBO Treatment Protocol Overview

Before we get into the particulars on small intestinal bacterial overgrowth, I want to give you an overview of our SIBO treatment protocol. This chart shows each step and gives you a clear picture of the timeframe:

Science gives us the path to solving SIBO, and we’ve found that using these therapeutics in this specific order gives us the highest resolution rate in the clinic. I’ll detail each of these steps later so you’ll know exactly what to do, but first, I’ll share what SIBO is and why remedying it is imperative.

SIBO: What You Need to Know

Small intestinal bacterial overgrowth is an inappropriately elevated level of bacteria in your small intestine 1. It’s normal to have some bacteria in this section of the gastrointestinal (GI) tract, but when the numbers start to increase, our symbiotic (mutually beneficial) relationship can be transformed into a detrimental one 2. Before we get into how SIBO impacts your health, I’ll take a detour through the small intestine to give you a better understanding of why SIBO can be so problematic.  

The Marvelous Small Intestine

I spend a lot of time reviewing the research and talking about the small intestine because I view it as the most important section of your entire digestive tract. As I discuss in Healthy Gut, Healthy You, the small intestine accounts for over 56% of our intestinal tract. At 22 feet long, its absorptive capacity is about the size of a tennis court. That huge surface area allows it to absorb about 95% of our nutrients, making the small intestine a pretty big deal.  

Since the small bowel is semi-permeable, meaning it allows certain substances to pass through its walls to enter the bloodstream, it needs some policing. In other words, the small intestine needs a way to allow essential nutrients and fluids to cross its barrier while preventing potentially harmful substances (like pathogens and toxins) from entering the bloodstream. It’s no wonder then that the largest mass of immune cells in your entire body lives in your small intestine.

At this point, you’re probably starting to imagine why dysfunction (like from a bacterial overgrowth) in the small intestine can wreak havoc on your health. Essentially, too many bacteria in the small intestine call your immune system to action 3. As it tries to kill the excessive bacteria, your immune system can damage the delicate intestinal barrier. When the intestinal wall is damaged, it becomes leaky, allowing pathogens, undigested food particles, and toxins to enter your bloodstream, where they should not be. 

This cycle of inflammation and leaky gut then sets off a cascade of events that re-triggers your immune system, creating more inflammation in your gut and throughout the rest of your body. This process can lead to malabsorption, various nutritional deficiencies (like vitamin B12 and iron), and an array of symptoms that aren’t just limited to your gut. 

SIBO Symptoms: Gut and Beyond

Of course, SIBO can cause obvious symptoms like malnutrition, unexpected weight loss or gain, flatulence, bloating, diarrhea, constipation, reflux, and nausea. But it can also give rise to a broad array of symptoms that you may not necessarily associate with poor gut health, including 4 5 6 7 8 9:

• Brain fog
• Poor memory
• Sleep disturbances
• Nerve pain
• Poor mood
• Thyroid autoimmunity
• Psoriasis, rosacea, and other skin conditions
• Restless leg syndrome
• Joint pain
• Hormonal alteration
• Fatty liver disease
• Metabolic disturbances

All of these symptoms of SIBO are very common, and the more you have, the higher the likelihood that you have SIBO. So, why do we get SIBO in the first place?

SIBO: Underlying Contributors 

I mentioned earlier that SIBO itself isn’t a disease, so you may be curious to know what causes the number of bacteria in your small intestine to increase. Though it can be hard to pinpoint the root of SIBO in most people, here are some potential underlying causes 10 11:

• Inadequate stomach acid, digestive enzymes, and/or bile: Not having enough of these digestive juices can lead to incomplete digestion, which leaves more food for bacteria to ferment. Fermentation produces gas (like methane) and other unfavorable substances that can contribute to symptoms. Your digestive juices are also the first line of defense for preventing pathogens (microbes that can make you sick) on your food from entering your small intestine.
• Poor motility related to certain disease states (gastroparesis), medications (like proton pump inhibitors), and food poisoning: Poor motility means your gut isn’t moving its contents through at a healthy rate. When motility is too slow, it allows food to remain in the GI tract longer than it should, which can encourage bacteria to hang out and eat (ferment) your food and reproduce.
• Structural issues related to gastric surgery, fistulas, adhesions, and diverticulosis:  Surgery or adhesions (a type of scar tissue) in the stomach or small intestine can create pockets in the small intestine that allow food—and the bacteria that eat—it to build up. Issues in the colon, like fistulas, adhesions, or diverticulosis, can allow bacteria from the large intestine (where most gut bacteria live) to regurgitate back into the small intestine, where they might take up residence. Any of these structural issues can impact motility.
• Immunodeficiency disorders: If you’re deficient in secretory IgA (a major antibody in the gut), it’s more difficult for the immune system to identify and kill excess bacteria in the small intestine. With little to keep them in check, such bacteria can become too numerous and cause problems. 

As you can see, there are many possible causes of SIBO. But I emphasize that it’s not necessary (or even possible in many cases) to know the root cause before starting the process of healing from SIBO. I say this because I’ve worked with many people who have been down the road of spending a lot of money and time trying to pinpoint the exact underlying condition. The result has typically been that these patients delay their treatment and go too long with a poor quality of life. 

I won’t deny that it’s often worth it to investigate and target the root cause(s) of SIBO to allow for more complete recovery and to prevent future recurrences. Partnering with a balanced healthcare provider can help you in this endeavor, but I want to make it clear that you don’t need to know the ‘why’ BEFORE starting a SIBO treatment protocol and feeling better. 

While we’re on the subject, you also don’t need to have a SIBO test before starting our 3-step treatment protocol. In the clinic, we’ve discovered that far more people respond to the safe, natural therapies we use to treat SIBO than those who actually have a positive SIBO test. That’s likely because many other gut issues tend to respond well to our treatments.

Think of it this way: If your SIBO test ends up being negative, you may still have SIBO (false negatives happen) or some other gut-related condition that the protocol can improve. But if you just skip the treatment because you don’t think you have SIBO, you might miss out on feeling better altogether. In the clinic, I tend to forgo testing and instead use my clinical judgment to treat my patients with science-based therapies.

My number one goal is to empower you with the tools you need to feel better.  The 3-step protocol I’m about to describe can safely help to remedy many gut-related (and other) symptoms, even if SIBO isn’t behind them. 

With that, let’s move on to the 3-step SIBO treatment protocol we use in the clinic to restore great gut health. 

3-Step SIBO Treatment Protocol

I’m a food-first healthcare provider, so it’s probably not surprising that dietary changes are where I begin when treating SIBO. This isn’t my preference for no reason. The research tells us that what we eat is a great jumping-off point, especially when it comes to healing from SIBO. 

Step 1: Low-FODMAP Diet and Lifestyle Reset

While there are several meal plans that may alleviate your SIBO symptoms, a low-FODMAP diet may provide the most bang for your buck 12 13 14 15.  

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. These are types of carbohydrates that can feed intestinal bacteria—the opposite of what we want to achieve when treating SIBO. A low-FODMAP diet restricts bacterial fuel, which serves to “starve” intestinal bacteria and discourage overgrowths. A 2021 study found that 4 weeks on a low-FODMAP diet shifted bacterial communities to a healthier balance, suggesting this type of diet may help to correct dysbiosis 16. 

When it comes to treating SIBO symptoms, I turn to irritable bowel syndrome (IBS) for clues because IBS is well-researched and closely tied to SIBO 17 18 19. Two meta-analyses (the highest-quality type of research) found that a low-FODMAP diet improved overall digestive symptoms, abdominal pain, and quality of life in IBS patients 13 15. And one review of 10 clinical trials found that a low-FODMAP diet improved symptoms in 50–80% of patients with symptoms of IBS 12. The same review reported profound improvements in the gut microbiota and overall gut health as a result of less leaky gut, inflammation, and histamine (markers of an overzealous immune system). 

Here’s a snapshot of a low-FODMAP diet:

Keep in mind that this is just an overview of a low-FODMAP diet. For more specifics on what you can eat and should avoid, Monash University offers a super-simple low-FODMAP app that gives detailed information about the FODMAP content of almost any food.  

I must stress that a low-FODMAP diet isn’t a long-term meal plan. Instead, it’s an investigative tool we use to determine your particular tolerance to certain foods. The way to go about it is to try a low-FODMAP diet for roughly 4–6 weeks. If your symptoms are improving, you can continue the diet for a total of 2–3 months. 

Once your symptoms have improved significantly, you can begin to systematically reintroduce the foods you eliminated to determine what you can and can’t tolerate. Most patients end up tolerating many foods upon reintroduction, so don’t be afraid to test the waters. The overall goal is to eat as broad a diet as possible while still managing your symptoms. 

It’s important for me to say that you don’t have to follow the diet perfectly to experience benefits. It’s more advantageous to avoid the stress and anxiety that can accompany trying to follow a meal plan to the letter. So, take a deep breath and do the best you can each day, and you’ll almost certainly see results. 

If you don’t see positive results on a low-FODMAP diet, your case may be more complex than most. You may benefit more from consulting with a knowledgeable healthcare practitioner who can help you get clarity on what’s going on.

In addition to eating a low-FODMAP diet, I encourage healthy lifestyle practices to enhance your progress and lead to quicker healing. Here are some suggestions to get you started:

• Aim for 7-8 hours of restful sleep every night.
• Manage or mitigate your stress.
• Nurture supportive relationships and healthy social connections.
• Spend time in the sun and in nature.
• Walk as much and as often as you can.
• Engage in a healthy amount of exercise.

A low-FODMAP diet and lifestyle reset may be all you need to resolve your SIBO symptoms. If that’s the case, that’s excellent! If you continue to hone your diet and keep up your healthy lifestyle behaviors, you’ll almost certainly maintain your improvements. If you’ve made some progress but still haven’t achieved great gut and overall health, then you can move on to step 2 and add probiotics.

Step 2: Probiotics

Probiotics can help to improve the balance of organisms in your gut, calm an overzealous immune system, and quell inflammation 20 21 22 23 24. They also help to clean out the “bad guys,” like pathogenic bacteria, fungi, and parasites, to promote a healthier microbial community in your gut 25 26.

While some healthcare providers recommend against using probiotics for SIBO, the research doesn’t support this practice. Numerous high-quality clinical trials confirm that probiotics can help treat SIBO. In fact, a meta-analysis showed that probiotics alone have about a 53% success rate for treating SIBO, which is about as effective as antibiotics alone 27. Even better, combining probiotics with antibiotics can bring the SIBO clearance rate to 85% 28. Probiotics may also be particularly helpful for people who haven’t responded to antibiotics for SIBO 29. 

An added bonus is that a low-FODMAP diet may work synergistically with probiotics. A 2020 randomized clinical trial with 50 IBS patients compared the effects of a low-FODMAP diet plus a placebo against a low-FODMAP diet plus a soil-based probiotic (Bacillus coagulans). Remember that IBS and SIBO are closely connected 17 18 19. After 8 weeks, both groups had improved symptoms and quality of life, but the low-FODMAP plus probiotics group had significantly more improvements in their IBS symptom scores 30. This highlights why our SIBO treatment plan starts with a low-FODMAP diet and then adds in probiotics.

So, which probiotics are best for SIBO? The great news here is that we have a lot of options. There’s no specific probiotic for treating SIBO, but the bulk of probiotic research suggests that using multiple strains of probiotics is the best way to go. One meta-analysis found that mixtures of multiple types of probiotics were more effective than single strains at treating IBS 31 32. And we’ve found that to be the case in the clinic. Most people don’t seem to achieve balance in their gut microbiome with just one strain of probiotic. We typically see the best results with patients who follow our triple-therapy protocol. This just means that we’re using the three most studied categories of probiotics in combination. 

Specifically, we combine what we call Category 1 (a Lactobacillus/Bifidobacterium blend) with Category 2 (Saccharomyces boulardii) and Category 3 (soil-based probiotics) If you tend to have a sensitive gut, you may want to start with just one of these, give it a couple of weeks, assess your tolerance, and then add another until you’re taking all 3. If you handle supplements well, you may want to start right off the bat with our Triple Therapy Probiotic sticks. Here’s the probiotic protocol we use in the clinic:

You’ll notice that I’ve recommended a minimum duration of 2 months on probiotics. This is because recent studies have found this to be the optimal time frame for seeing peak improvements with probiotics 33 34. You’ll likely notice improvements within a few weeks of taking probiotics, but you may not see the full benefit until 2 or even 3 months in. So, this is a reminder that if you’ve tried probiotics in the past without success, it could be that you stopped taking them too soon. Implementing the triple-therapy approach for at least a couple of months may make all the difference. If you try this method and still don’t find it beneficial, then you can stop taking probiotics and know that you’ve fully explored this therapy.

Completing steps 1 and 2 will likely bring significant relief, but if you still have bothersome symptoms, move on to step 3 to layer on antimicrobial therapy. 

Step 3: Antibiotics or Herbal Antimicrobials

If you’ve been pretty consistent with diet, lifestyle, and probiotics, but your symptoms persist, it may be time to try herbal antimicrobials. Just like with probiotics, we have options here. One option is to get a prescription for an antibiotic called rifaximin (Xifaxan). If you’re hesitant to use antibiotic therapy, let me alleviate your fears by sharing that rifaximin is effective and safe. In one study, it eliminated SIBO in 67% of patients 35, which is pretty impressive. The drawback here is that it requires a prescription from your healthcare provider, and it’s expensive if your health insurance doesn’t cover it. 

If you’re sure you’d like to avoid antibiotics, herbal antimicrobials are another option. They are available over-the-counter, work at least as well as rifaximin for treating SIBO, and they can relieve IBS symptoms 36 37. Herbal antimicrobials may also have added benefits, like lowering inflammation and curbing depression 38 38 39. Plus, herbal options may also combat other microorganisms, like the fungus Candida 40 and protozoan parasites 41, whereas antibiotics work only against bacteria 42. One drawback to herbal antimicrobials is that you have to take them longer (about 2 months) than a course of antibiotics (about 14 days).

In the clinic, we use two herbal antimicrobial formulations for the first month and two different ones for the second month. As I share in Healthy Gut, Healthy You, these formulas are designed to address SIBO and any infections from fungi (e.g. Candida), Helicobacter pylori (stomach bacteria), Blastocystis hominis (intestinal parasite), Giardia (intestinal parasite), other protozoan parasites, and intestinal worms, all of which can contribute to your symptoms.

Here’s a chart detailing the month-1 antimicrobial protocol:

This chart details the month-2 antimicrobial protocol:

As always, you should speak with your healthcare provider before implementing new dietary supplements.

Most of my patients tolerate herbal antimicrobial therapy well, but there’s still the potential to feel unwell in the short term. While this can be frustrating, these symptoms can signal that the therapy is working. Here’s what happens: When herbal antimicrobials kill the “bad guys,” it can trigger the immune system, which may increase your symptoms. If this occurs, it usually goes away after several days. But if you’re still noticing an uptick in your symptoms after about a week, it’s probably best to stop the therapy and continue on with diet, lifestyle, and probiotics if those are working well for you. 

The bottom line is that research supports using these three steps—a low-FODMAP diet, probiotics, and antibiotics or herbal antimicrobials—in this specific order to treat SIBO. Incorporating all three will likely eliminate approximately 85% of your SIBO and significantly improve your symptoms. 

That said, if those three steps aren’t enough (i.e. you’re still not feeling well or you think you’re almost but not quite there), we have an additional science-based SIBO treatment option to check out: the elemental diet.

Bonus Step: The Elemental Diet

The elemental diet is a hypoallergenic, anti-bacterial, anti-inflammatory meal replacement shake. The nutrients (carbohydrates, proteins, and fats) in it are already partially or completely broken down into easily absorbed units that give your digestive system the opportunity to rest and heal. 

The elemental diet has long been prescribed for treating inflammatory bowel diseases (like Crohn’s disease) because it tends to lower inflammation, reverse the underlying causes of autoimmunity, and prevent flare-ups 43 44 45 46. There’s less research on using elemental diets to treat SIBO, but one study had IBS patients with bacterial overgrowth follow an elemental diet exclusively for two weeks. Of those patients, 80% had normal breath test results and 65% had improved IBS symptoms 47. 

Does this mean you should try to eat nothing but this liquid meal replacement shake for 2 weeks or longer? Not necessarily. In fact, we typically recommend using the elemental diet as a 2–4-day reset. Once you’ve completed the initial reset, you can then consider using a hybrid approach of replacing one or two regular meals per day and eating normally for the remainder. 

You may be wondering if you need to complete the entire 3-step SIBO treatment protocol before using the elemental formula. And the answer is no, you can start off with a 2–4 day elemental diet reset before starting with step 1. But you can also use the elemental formula at any point during or after the process. While this hasn’t been formally studied, we’ve found it to be highly effective for our patients in the clinic, and it gives you an additional option for long-term SIBO success.

Fortunately, there are a lot of simple, science-based strategies you can use to improve your SIBO symptoms. I’ve shared in this video how uncomplicated it can be to heal from SIBO.

SIBO Treatment Made Safe, Simple, and Effective 

SIBO simply means you have too many gut bacteria in your small intestine. This type of bacterial overgrowth can increase inflammation, induce leaky gut, and impact your ability to absorb nutrients from your food. Digestive symptoms are common with SIBO, but you may also experience symptoms like brain fog, fatigue, skin issues, poor mood, and joint pain.  It’s often routine to test for SIBO or look for root causes when you have gut issues, before you begin treatment. However, knowing your test results and rooting out the cause(s) of your SIBO are usually unnecessary. There’s no reason to delay your healing in pursuit of these answers, which may never bear fruit.  

If you have IBS or otherwise suspect you have SIBO, you have the option to consider (ideally with support from your healthcare provider) our 3-step, science-based SIBO treatment protocol. First, you’d set the stage with a low-FODMAP diet to reduce the foods for the bacteria to ferment and reduce your symptoms. Then, you’d add in multi-strain probiotics to support your microbiome and start eliminating the overgrowth. Finally, you’d bring in antibiotics or herbal antimicrobials to finish the job. And if you want some extra oomph, you can start with 2–4 days of a full or partial elemental diet before step 1, or you can use the elemental formula at any point during or after treatment.

Each of these steps is safe and effective for eliminating SIBO and treating many other gut-related conditions that could be contributing to your symptoms. Layering the therapies in this step-by-step process can lead to quicker resolution of your symptoms and more complete healing.

That said, if you’ve completed this 3-step process (with or without an elimination diet) but continue to have lingering symptoms, you could have something more complex going on. Please feel free to contact us for an appointment at the Ruscio Institute for Functional Health; we’d love to help you get to the bottom of it.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.