Articles

Evidence based

Evidence Based

This article is based on scientific evidence, written by experts and fact checked by experts.

Our team of licensed nutritionists and dietitians strive to be objective, unbiased, honest and to present both sides of the argument.

This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers.

Small Intestinal Bacterial Overgrowth (SIBO): 3-Step Treatment Guide

Written by Dr. Michael Ruscio, DC on April 7, 2025

Written by Dr. Michael Ruscio, DC on April 7, 2025 — Reviewed by Hannah Wright

• Overview|
• What You Need to Know|
• Step 1: Low-FODMAP Diet|
• Step 2: Probiotics|
• Step 3 (If Needed): Antibiotics or Herbal Antimicrobials|
• Bonus: The Elemental Diet|

It’s common in our clinic to meet folks who have struggled for years with symptoms like brain fog, poor sleep, depression, skin issues, joint pain, and digestive discomfort. To find relief, many have tried numerous tests, supplements, and medications, but they have largely been unable to heal completely. 

If this sounds like you, small intestinal bacterial overgrowth, or SIBO, could be behind your symptoms. Luckily, SIBO treatment doesn’t have to be complicated.

What is SIBO? 

Small intestinal bacterial overgrowth (SIBO) is a harmfully high 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 with our gut bacteria can turn harmful 2. 

Before we get into SIBO treatment, I’ll take a detour through the small intestine to give you a better understanding of why SIBO can be so problematic.  

What Is the Small Intestine?

The small intestine is arguably the most important section of the entire digestive tract. 

As I discuss in my book, Healthy Gut, Healthy You, the small intestine accounts for over 56% of the intestinal tract. At 22 feet long, its absorptive surface area—including numerous folds and countless microscopic finger-like projections called villi that are covered in hair-like extensions called microvilli—is about the size of a tennis court. That huge surface area allows the small intestine to absorb about 95% of the nutrients in our food and beverages, making this section of the gut a pretty big deal.  

Since the small intestine is semi-permeable, meaning it allows certain substances to pass through its walls to enter the bloodstream, it needs some policing. That’s where the immune system comes in: It allows essential nutrients and fluids to cross the small intestinal barrier while preventing infectious organisms 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.

When the numbers of bacteria get too high in the small intestine, the immune system goes into overdrive as it tries to regain balance. An immune system in overdrive will cause inflammation, which, when it goes on for long, produces chronic symptoms that let us know it’s time for SIBO treatment. 

Symptoms of SIBO

SIBO can cause GI symptoms like flatulence, bloating, belly cramping, diarrhea, or constipation 3. It’s very common in people with irritable bowel syndrome (IBS) 4, and it can occur in those with inflammatory bowel disease (IBD) and celiac disease. 

SIBO can also occur with symptoms or conditions you may not associate with poor gut health, including:

• Chronic fatigue syndrome 5
• Mood problems like stress, anxiety, and emotional sensitivity 6
• Brain fog 7
• Rosacea and psoriasis 3
• Restless legs syndrome 3
• Joint pain 3
• Headache
• Hypothyroidism 3 8
• Non-alcoholic fatty liver disease 3
• Diabetes 3

All these symptoms can be mistaken for other conditions, but the more of them you have, the more likely it is that you need SIBO treatment. So, why do we get SIBO in the first place?

Causes of SIBO

Though it can be hard to pinpoint the root of SIBO in most people, here are some potential underlying causes:

• Too little stomach acid, digestive enzymes, or bile 1: If these digestive juices are too low, your body can’t fully break down food. This leaves more for bacteria to feed on, or ferment. Fermentation produces gas (like methane) and other substances that may lead to symptoms. Your digestive juices also kill harmful microbes in your food before they reach your small intestine. 
• Poor motility 1: If your gut isn’t moving food through at a healthy rate, it stays in your system too long. This can happen as a result of certain conditions (like gastroparesis), medications (such as proton pump inhibitors), or food poisoning. When food lingers, bacteria have more time to feed on (ferment) it, multiply, and cause problems like gas and discomfort.
• Leaky gut 9: Also called increased intestinal permeability, a leaky gut drives inflammation in the gut. Inflammation can upset the balance of gut microbes, allowing bacteria to overgrow in the small intestine. 
• Structural issues 1: Changes in the structure of the digestive system related to surgery, abnormal connections (fistulas), scar tissue (adhesions), or conditions like diverticulosis can create pockets where food and bacteria collect. In some cases, bacteria from the large intestine (where most gut bacteria live) move backward into the small intestine, where they don’t belong. These issues can also slow down digestion, making things worse.

Now that you know about the many possible causes of SIBO, let’s move on to the 3-step SIBO treatment protocol we use in the clinic to restore gut health. 

3-Step SIBO Treatment Protocol

Before we get into the particulars of small intestinal bacterial overgrowth (SIBO) treatment, here’s an overview of the SIBO treatment protocol we use at the clinic. 

I’m a food-first healthcare provider, so I start with dietary changes when treating SIBO. My clinical experience and a body of research show that food and probiotics form a great foundation for healing from SIBO. 

Step 1: Low FODMAP Diet

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 when treating SIBO. A low FODMAP diet restricts the foods bacteria love to ferment, which starves them and discourages overgrowth. 

When it comes to treating SIBO symptoms, I turn to the well-researched irritable bowel syndrome (IBS) for clues because IBS and SIBO often go hand-in-hand 4. IBS research has found that a low FODMAP diet can alleviate the symptoms of both IBS and SIBO 10. 

Here’s an overview of a low FODMAP diet:

For more specifics on what you can eat and should avoid, Monash University offers a simple, free low FODMAP app that gives detailed information about the FODMAP content of almost any food.  

Although it can be safe to follow for up to a year 11, a low FODMAP diet is limited and shouldn’t be a long-term meal plan. At the clinic, we usually have clients try a low FODMAP diet for 4–6 weeks. As soon as they learn to follow the diet, they also start taking probiotics.

Step 2: Probiotics

Probiotics can help balance gut bacteria, reduce inflammation, and eliminate harmful microbes 12. A low FODMAP diet works well with probiotics, as shown in a study where patients using both had greater symptom improvements 13. 

Although some healthcare providers advise against probiotics for SIBO, research shows they can be as effective as antibiotics alone (53% success rate) 14 and even more effective when combined with antibiotics (85% clearance rate) 15. Probiotics may be ideal for SIBO patients who haven’t responded to antibiotics 16. 

There’s no single best probiotic for treating SIBO, but using multiple strains is more effective than using single strains for treating IBS 17 18. 

We’ve found that to be true for SIBO clients in the clinic, so we follow a triple-therapy protocol, combining these three most studied probiotic categories:

• Lactobacillus/Bifidobacterium blends
• Saccharomyces boulardii (a beneficial yeast)
• Soil-based Bacillus species

Our clients with sensitive digestion often start with just one of these, usually the Lacto/Bifido blend. After tolerating it well for a few days, they add another, one at a time, until they’re taking all three. 

We see the best results when clients take all three categories at once, as shown in the following chart.

We’ve made this convenient with our Triple Therapy Probiotic sticks.

Some people start feeling better within a few weeks of taking probiotics, but it can take 2 to 3 months to see the full benefits 19 20. If probiotics didn’t work for you in the past, you may have stopped too soon. However, if you’ve taken them for up to 3 months with no improvement, it’s ok to stop.

A low FODMAP diet and probiotics are often all our clients need to resolve their SIBO symptoms. They then continue to expand and hone their diet and keep up their healthy lifestyle behaviors to maintain their improvements. 

Don’t Forget a Healthy Lifestyle

A healthy lifestyle is key to making this work. Along with a low FODMAP diet and probiotics, I recommend healthy habits to speed up healing and improve results. Here are some guidelines we provide for our clients:

• Aim for 7–9 hours of restful sleep every night.
• Manage 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.

If our clients have followed a low FODMAP diet, taken probiotics, and improved their lifestyle without having reached great gut health and overall well-being, we move on to step 3: antimicrobial therapy.

Step 3: Antibiotics or Herbal Antimicrobials

Just like with probiotics, we have antimicrobial options for SIBO treatment. One option is to get a doctor’s prescription for an antibiotic called rifaximin (Xifaxan). For those who are hesitant to use antibiotic therapy, rifaximin is effective and safe, with the potential to eliminate SIBO in 67% of sufferers 21. What’s even more impressive is that combining probiotics with antibiotics can clear SIBO 85% of the time.

The main drawback of rifaximin is that it requires a prescription, and it’s expensive if your health insurance doesn’t cover it. 

For those who are sure they’d like to avoid antibiotics, herbal antimicrobials are another option. They are available over-the-counter and can work at least as well as rifaximin for treating SIBO 22. Herbal antimicrobials may also combat other microorganisms, like the fungus Candida 23 and protozoan parasites 24, whereas antibiotics work only against bacteria 25. 

The main drawback of herbal antimicrobials is that you have to take them longer (about 2 months) than a course of antibiotics (about 14 days).

In the clinic, while our clients take probiotics, we also have them take two herbal antimicrobial formulas for the first month and two different ones for the second month, as follows: 

These formulas help treat SIBO along with other possible infections, like fungal overgrowth (Candida), stomach bacteria (Helicobacter pylori), intestinal parasites (Blastocystis hominis and Giardia), other protozoa, and intestinal worms, all of which can add to your symptoms.

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

Most of our clients handle herbal antimicrobial therapy well, but some may feel worse at first. This is usually a sign that the treatment is working, as the immune system reacts to dying bacteria. Symptoms should improve after several days, but if they persist longer than a week, stopping the therapy and focusing on diet, lifestyle, and probiotics may be best. 

The bottom line is that the most effective SIBO treatment follows three key steps: a low FODMAP diet with probiotics and, if necessary, either antibiotics or herbal antimicrobials. This approach typically clears SIBO in most cases. However, if symptoms persist, a fourth option to consider is the elemental diet, another science-backed alternative.

Bonus Treatment Step: The Elemental Diet

The Elemental diet is a hypoallergenic, anti-bacterial, anti-inflammatory meal replacement shake. The macronutrients (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. 

Elemental diets have long been prescribed for treating inflammatory bowel diseases (like Crohn’s disease) because these formulas can lower inflammation, reverse the underlying causes of autoimmunity, and prevent flare-ups 26 27. 

There’s less research on using elemental diets to treat SIBO, but one study had 93 IBS patients with SIBO follow an elemental diet exclusively for two weeks. Of those patients, 80% had normal breath test results and 65% had improved IBS symptoms 28. 

Following an elemental diet full-time takes commitment, but I’ve seen this approach, done for 1–3 weeks, work very well for SIBO. To weather the potential side effects of bacterial die-off, I strongly recommend working with a healthcare provider rather than going this long on an elemental diet alone.

However, we’ve also found good results when clients use an elemental diet for 2–4 days as a gut reset and then continue to use it to replace one or two meals a day until symptoms resolve. This is an approach people can use safely on their own.

As you can see, there are simple, safe, science-based strategies you can use to improve your SIBO symptoms. Indeed, it can be straightforward to heal from SIBO.

SIBO Treatment Made Safe, Simple, and Effective 

SIBO simply means you have too many bacteria in your small intestine. This type of bacterial overgrowth can cause a wide array of symptoms, some digestive and others not. If you suspect you have SIBO, you might consider (ideally with support from your healthcare provider) our 3-step, science-based SIBO treatment protocol. 

If you’ve completed this 3-step process (with or without an elemental 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 clients 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. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.