From Breath Test to Treatment Plan: Managing SIBO, IMO, and ISO Effectively
Small Intestinal Bacterial Overgrowth (SIBO), Intestinal Methanogen Overgrowth (IMO), and Intestinal Sulfide Overproduction (ISO) are all gastrointestinal conditions characterized by an imbalance in the gut microbiota, which is what scientists call the unique combination of microorganisms that exist in your gut. These microorganisms include bacteria and archaea (another type of single-celled microorganism that is distinct from bacteria). Even though the thought of these tiny organisms living inside your body might seem disturbing, their presence is not inherently bad. In fact, when they are present in the right balance they are essential to healthy gut function, aiding you in digesting food and absorbing the life-sustaining nutrients it provides.
However, when your gut’s normal function becomes disrupted or dysregulated, the balance of your microbiota can begin to shift, resulting in an overgrowth or overproduction of one or more of these organisms, often with far-reaching consequences. People with SIBO, IMO, and ISO can experience uncomfortable and debilitating symptoms like bloating, abdominal pain, gas, nausea, diarrhea, constipation, and even malabsorption of nutrients. All of these symptoms can seriously affect your quality of life, and if left untreated, prolonged vitamin and mineral deficiencies caused by malabsorption can even damage bones and the nervous system.
Diagnosis of SIBO, IMO, and ISO
If you’ve been experiencing some of the symptoms mentioned above, you’re not alone. Recent studies show that up to two-thirds of Americans report having recurrent digestive issues like bloating, constipation, and diarrhea. And while the exact prevalence of SIBO, IMO and ISO in the population is unknown, data suggest that millions of Americans are likely living with these conditions, whether diagnosed or undiagnosed. Since gastrointestinal (GI) disorders often present with similar symptoms and many GI conditions are not currently identifiable through specific testing, patients often endure a lengthy, frustrating, and costly search for answers.
Fortunately, there is a straightforward, scientifically validated at-home breath test to help identify patients with SIBO, IMO, and ISO: The Trio-Smart 3-Gas Breath Test. Through extensive research, scientists know that certain microorganisms in your gut produce three specific gases that can help you figure out what’s going on inside you: hydrogen, methane, and hydrogen sulfide. Excess levels of one or more of these gases could indicate a microbiota imbalance, with each gas pointing at a specific type of overgrowth or overproduction: hydrogen correlating with SIBO, methane correlating with IMO, and hydrogen sulfide correlating with ISO. Breath testing allows you to obtain accurate measurements of the levels of each gas in your gut, which can be a key step in your quest to get an accurate diagnosis. With this diagnosis in hand, you can then work with your healthcare providers to begin a treatment or management program aimed at your specific needs.
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Let’s take a deep dive and look at each of these conditions and all of the treatment and management options currently available.
SIBO Treatment & Management
Small Intestinal Bacterial Overgrowth (SIBO) is a condition characterized by an abnormal increase in the number and type of bacteria in the small intestine. Normally, the small intestine contains relatively few bacteria compared to the large intestine (colon). But a variety of factors–including complications from abdominal surgery, structural problems or blockages of the small intestine, Crohn’s disease, scleroderma, celiac disease, diabetes, and IBS–can disrupt the normal motility (movement of food) and function of your gut. Especially if left undiagnosed or untreated for prolonged periods, these disruptions can result in dysbiosis, which means that your gut’s microbiome is out of balance. This in turn can cause some or all of those debilitating symptoms you are experiencing: bloating, abdominal pain, gas, abdominal distension, indigestion, constipation, and diarrhea. Of these symptoms, bloating is the most commonly reported symptom of patients diagnosed with SIBO.
Since we know that excessive levels of hydrogen can be an indicator of abnormally elevated bacterial counts in the small intestine, this provides us with a way to test for this type of overgrowth. The Trio-Smart 3-Gas Breath Test collects samples of your breath over a period of time. When you send back your sample, the lab processes it and measures the level of hydrogen gas present, and this measurement is compared against known standards. The threshold of hydrogen is calculated by adding 20 ppm (parts per million) to the baseline. A rise in hydrogen levels by 20 ppm or more within 90 minutes is supportive of SIBO.
This breath test result is a significant piece of the puzzle that your healthcare provider can use, along with other clinical evaluative criteria, to make a SIBO diagnosis. And with this diagnosis in hand you can begin a treatment plan. The American College of Gastroenterology (ACG) Guideline for SIBO suggests the use of antibiotics in symptomatic patients to eradicate overgrowth and resolve symptoms. Antibiotics like rifaximin–which studies have so far shown to be the most effective antimicrobial for use in patients with SIBO–help your body curtail the overgrowth of bacteria, thereby aiding your gut in restoring the microbiome to a more balanced state. Once the bacterial overgrowth is reduced, you will likely start to feel the severity and frequency of your symptoms subside.
Your healthcare team may also suggest you engage in some diet modification aimed at promoting a more healthy microbiome that will reduce the likelihood of your SIBO worsening or recurring. Scientists now know that certain foods can encourage bacterial overgrowth either by disrupting the normal motility of your gut or by supplying these microorganisms with excess nutrients they need to thrive and multiply–much like adding fuel to a fire. So, it is often beneficial for patients to avoid those foods and instead choose alternatives that are part of a low-FODMAP diet or are consistent with low-fermentation eating.
In severe cases of SIBO, or in cases where antibiotics have proven to be ineffective or are poorly tolerated, your doctor may recommend an elemental diet designed to starve the bacteria in your gut in order to gain the upper hand in your fight against their excessive overgrowth. All of these eating plans are discussed in more detail later in this article.
IMO Treatment & Management
Intestinal Methanogenic Overgrowth (IMO) is an overgrowth of methane-producing archaea in the small and large intestines. This condition was previously called “methane SIBO.” However, that term isn’t quite accurate since the methanogens (methane-producing microorganisms) can cause an overgrowth in both the large and small intestines, and they are actually archaea, not bacteria. Archaea are a group of single-celled organisms lacking a defined nucleus, and they are a distinct form of life, separate from bacteria, plants, animals and fungi. They often thrive in extreme environments like hot springs, salt lakes, or acidic environments, and some types of archaea are known to live in your gut, where they play a role in digestion and metabolism.
Patients with IMO often experience similar symptoms to those with SIBO, such as bloating, abdominal pain, flatulence, constipation, diarrhea, and nausea. Like SIBO, the most reported symptom of IMO is bloating. However, IMO patients show a notably higher prevalence of moderate to severe constipation versus control groups, while tending to show a lower prevalence of diarrhea and nausea.
Since the hallmark of IMO is the presence of these methane-producing archaea, breath testing with the Trio-Smart 3-Gas Breath Test can help determine whether you have IMO by measuring the levels of methane in your collected samples. The threshold for methane is always 10 ppm, so if any methane levels exceed 10 ppm during the test, your results will be marked as abnormal. Interestingly, the correlation between methane gas and constipation is so strong that the degree to which your methane levels are elevated beyond normal has been shown to be a reliable predictor of how bad your constipation is.
Like SIBO, the ACG clinical guidelines suggest the use of antibiotics to reduce the methanogenic overgrowth. However, evidence strongly suggests that a multi-antibiotic approach–specifically a combination of rifaximin and neomycin–achieves significantly better results than treatment from a single antibiotic. In a study conducted by the GI Motility Program at Cedars-Sinai Medical Center in Los Angeles, California, and published in the Journal of Clinical Gastroenterology, researchers found that 87% of subjects taking a combination of rifaximin and neomycin eradicated the methane in their breath tests, while only 28-33% of subjects taking only rifaximin or neomycin were able to do so.
The reason for this is due to the source of the methanogenic overgrowth: the archaea. Since archaea have different cellular structures and metabolic pathways from bacteria, they are less responsive to single-antibiotic treatments. But, rifaximin and neomycin team up well together with complementary actions. Rifaximin primarily targets the bacterial species in your gut, reducing the hydrogen production that the archaea need, while neomycin targets the archaea themselves. By simultaneously destroying the methanogens and shutting down the bacterial component feeding them, this multi-antibiotic approach achieves better results, lessening the methane production more quickly and alleviating your symptoms faster.
Like SIBO, you may need to engage in some diet modification with the intent of reducing sources that feed the methane-producing microorganisms in your system. Limiting fermentable carbohydrates that indirectly support methanogen populations and reducing or avoiding foods that induce constipation, specifically insoluble fibers such as whole grains and nuts, are some steps you may be asked to take. More information on low-fermentation eating and other diet plans can be found later in this article.
ISO Treatment & Management
Intestinal Sulfide Overproduction (ISO) is a condition that results in the overgrowth of sulfide-producing organisms, most commonly bacteria from the Desulfovibrio, Bilophila, and Fusobacterium genera. Factors like altered gut motility, excessive consumption of sulfur-containing foods, bile acid imbalances, and other issues that are known to lead to a microbial imbalance allow these sulfide-producing microbes to flourish, resulting in an overproduction of hydrogen sulfide. Elevated levels of hydrogen sulfide can irritate and damage the intestinal lining, causing inflammation and increased gut permeability (“leaky gut”).
Patients with ISO experience many similar symptoms to those with SIBO, including bloating, abdominal pain, flatulence, nausea, and diarrhea. However, diarrhea may be the most telling of all of those shared symptoms, as emerging research is finding that increased levels of hydrogen sulfide are strongly correlated with an increased prevalence of diarrhea, in the same way that higher methane concentrations correlate to a higher prevalence of constipation in IMO patients.
Historically, the presence of hydrogen sulfide-related overgrowths has often been unrecognized, misunderstood, or underdiagnosed. One of the primary reasons for this is that, until the Trio-Smart 3-Gas Breath Test became available, no breath test measured the levels of hydrogen sulfide in your gut, so patients with abnormal hydrogen sulfide levels may have appeared “normal” on previous breath tests. In fact, Dr. Mark Pimentel, MD, the foremost expert on SIBO, IMO, and ISO, and the Executive Director of the Medically Associated Science and Technology Program at Cedars-Sinai estimates that “25% of patients who appear normal on hydrogen and methane tests could have elevated hydrogen sulfide levels and associated GI complications.”
The Trio-Smart 3-Gas Breath Test remains the only breath test on the market that measures hydrogen sulfide levels, and is therefore the only one that can help you and your healthcare providers determine whether an ISO diagnosis is appropriate for you. When measured by a breath test, the threshold for hydrogen sulfide is 3 ppm. Levels of hydrogen sulfide that are 3 ppm or more at any point during the breath test are considered excessive and are potentially associated with ISO.
Similar to the other conditions discussed, treatment with antibiotics like rifaximin is generally recommended for ISO in order to reduce the overgrowth of hydrogen sulfide-producing bacteria in your gut.
Additionally, some studies have shown that bismuth subsalicylate (BSS)--commonly known as Pepto Bismol–has proven effective at reducing hydrogen sulfide levels and normalizing the rate of intestinal motility. One study published in Gastroenterology, the official journal of the American Gastroenterological Association, found that treatment of subjects with bismuth subsalicylate produced a >95% reduction in fecal hydrogen sulfide release, concluding that it could play a role in lessening the deleterious effects caused by excessive hydrogen sulfide. However, if you have ISO and your hydrogen sulfide overproduction is caused by an overgrowth of bacteria, managing your gas levels solely with BSS does not address the root cause. So, pairing antibiotic treatment with regular doses of BSS is generally more effective than BSS alone.
Diet modification is also usually involved when treating patients with ISO. Your doctor may suggest you adhere to low-fermentation eating long-term, while also adding a specific emphasis on a low-sulfur diet. By avoiding foods that are rich in sulfur you can help to limit one of the two building blocks used by bacteria to create hydrogen sulfide. More on these eating plans and diets can be found in the following section.
Dietary Approaches to Managing SIBO, IMO & ISO
Low-FODMAP Diet: A Short-Term Elimination Approach
One of the most widely recognized dietary approaches for SIBO and related gut conditions is the Low-FODMAP Diet, developed by researchers at Monash University. FODMAP stands for Fermentable, Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. This diet focuses on reducing fermentable carbohydrates that are poorly absorbed in the small intestine and feed bacteria there, leading to excessive gas production and bloating. By temporarily eliminating high-FODMAP foods, many individuals experience a significant reduction in symptoms.
However, the Low-FODMAP Diet is usually recommended in conjunction with other treatments like antibiotics, and it is not intended to be a permanent solution. Instead, it is typically followed for four-to-six weeks (or the length of time your doctor recommends based on your personalized treatment plan), after which foods are systematically reintroduced to identify individual triggers. Long-term restriction of FODMAPs can negatively impact the gut microbiome, limiting its diversity and effectiveness while also leading to a potential for nutrient deficiencies.
Foods to Avoid (High-FODMAP):
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Garlic and onions
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Wheat, rye, and barley (in large amounts)
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Milk, yogurt, and soft cheeses (lactose)
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Apples, pears, watermelon, and stone fruits
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Beans, lentils, and chickpeas
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Sweeteners like sorbitol, mannitol, and xylitol
Foods to Choose (Low-FODMAP):
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Carrots, spinach, zucchini, and bell peppers
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Bananas, blueberries, grapes, and oranges
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Lactose-free milk, hard cheeses, and plant-based milks (like almond)
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Gluten-free grains (rice, oats, quinoa)
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Chicken, eggs, tofu, and most fish
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Olive oil and small amounts of maple syrup
Low-Fermentation Eating: A Sustainable Long-Term Strategy
Due to the limitations and nutritional concerns associated with indefinite adherence to the Low-FODMAP Diet, Dr. Mark Pimentel developed a more sustainable dietary approach: Low-Fermentation Eating (LFE). LFE focuses on reducing fermentable foods while emphasizing protein-rich meals to minimize bacterial overgrowth.​
One key principle of low fermentation eating is spacing meals four to five hours apart to allow the Migrating Motor Complex (MMC) to sweep bacteria out of the small intestine between meals. This is particularly important for preventing the recurrence of SIBO and IMO, as poor motility is a major contributing factor in bacterial overgrowth. Many people find this approach easier to maintain than Low-FODMAP diets, and the nutritional diversity helps to maintain a more balanced and robust microbiome, making it a more practical long-term solution for sustainable gut health.
Foods to Avoid:
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Beans and legumes (lentils, chickpeas, black beans)
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Cruciferous vegetables (cabbage, Brussels sprouts, broccoli, cauliflower, kale)
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Whole grains (whole wheat breads, multigrain breads, oats)
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Dairy products with lactose (milk, yogurt, soft cheeses)
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Certain fruits (apples, pears, bananas)
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Sweeteners (sucralose/Splenda™, sugar alcohols like sorbitol, xylitol)
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Gums and thickeners (gum Arabic, xanthan gum, carrageenan)
Foods to Choose:
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Refined carbohydrates: White bread (sourdough, French, potato bread), white rice
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Proteins: Beef, chicken, fish, pork, eggs
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Non-cruciferous vegetables: Peppers, tomatoes, carrots, cucumbers, zucchini, squash, eggplant, peas, mushrooms, potatoes, sweet potatoes
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Fruits: Most fruits (limit apples, pears, bananas)
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Dairy: Lactose-free milk, hard cheeses (cheddar, Parmesan)
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Nuts and seeds: Almonds, walnuts, pecans, macadamia nuts, sunflower seeds, pumpkin seeds
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Oils and fats: Olive oil, coconut oil, butter (in moderation)
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Meal Timing Recommendations:
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Structured meals without frequent snacking
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At least 4-hour gaps between meals
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Avoid late-night eating to support gut motility
Elemental Diet: A Powerful Gut Reset
For those with severe or recurrent SIBO, IMO, or ISO, the elemental diet can be an effective treatment option. The elemental diet consists of a liquid-only formula that provides fully broken-down nutrients (such as amino acids, simple carbs, and fats) in forms that are easily absorbed in the gut without requiring fermentation. By depriving bacteria of their food source, the elemental diet essentially starves out bacterial overgrowth while still providing essential nutrition.
Studies show that the elemental diet has a high success rate, with some reports indicating that up to 80% of individuals experience a significant reduction in bacterial overgrowth after following the diet for two to three weeks. However, because it requires strict adherence to a specific liquid diet, it can be challenging for some people due to issues like taste, cost, lifestyle challenges, and calorie restrictions. So, it is generally more often used with patients when antibiotics haven’t proven effective or cannot be tolerated.
​​​It’s important to note that the elemental diet is something that should only be attempted under the care and supervision of your healthcare provider to ensure that you are receiving the correct balance of nutrients to maintain safety and effectiveness.
Low-Sulfur Diet: A Useful Addition for ISO Patients
Foods to Avoid (High in Sulfur):
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Cruciferous vegetables: Broccoli, cauliflower, cabbage, Brussels sprouts, kale, bok choy, arugula
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Alliums (very high in sulfur): Garlic, onions, leeks, shallots, chives
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Animal proteins (especially high-sulfur): Eggs (especially yolks), red meat (beef, lamb, pork), organ meats, shellfish
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Legumes and soy products: Lentils, beans (black, kidney, pinto, etc.), soy milk, tofu, tempeh
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Nuts and seeds (high in sulfur amino acids): Almonds, cashews, walnuts, Brazil nuts, sunflower seeds, sesame seeds
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Dried fruits and processed foods with sulfites: Dried apricots, raisins, wine, cider, packaged sauces, deli meats (if preserved with sulfites)
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Additives and preservatives: Sulfites, sulfur dioxide (check ingredient labels)
Foods to Choose (Low in Sulfur):
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Fruits: Apples, berries, citrus fruits, grapes, melons, peaches, plums
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Vegetables (low-sulfur): Carrots, cucumbers, zucchini, lettuce, spinach, bell peppers, celery, green beans, squash, eggplant, potatoes
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Proteins (low-sulfur in moderation): Chicken breast (small portions), white fish (e.g., tilapia, cod), turkey breast, plant-based protein powders (pea or rice-based)
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Grains and Starches: White rice, oats, quinoa, gluten-free bread, white bread, pasta (non-enriched)
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Dairy (low-sulfur options): Lactose-free milk, unsweetened almond milk, coconut milk, hard cheeses (in moderation)
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Fats and Oils: Olive oil, coconut oil, avocado oil
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Beverages: Herbal teas (peppermint, ginger), water, diluted fruit juices
Additional Management Options: Gut Health Beyond Medication & Diet
For those looking for additional methods of managing their condition, or for those patients where traditional methods like antibiotics are not viable, there are a few other options to consider:
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Prokinetics: Since bacterial overgrowth often recurs, some practitioners recommend prokinetics, which are a type of medication or supplement that helps stimulate or improve the motility in the gastrointestinal tract. By helping your gut maintain regular motility, you may reduce the likelihood that your overgrowth returns. Prescription prokinetics include low-dose erythromycin, prucalopride, and tegaserod. Natural prokinetics include ginger, MotilPro, and Iberogast.
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Managing Stress: Stress plays a significant role in gut health, as chronic or severe stress can disrupt your normal gut motility and contribute to microbial overgrowth. Incorporating stress management techniques like breathwork, vagus nerve activation exercises, yoga, and meditation can help you manage your stress levels and may have a positive impact on your gut health.
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Lifestyle Habits: Other lifestyle habits could also positively impact your gut function and overall health. Chewing food thoroughly, getting adequate sleep, engaging in regular movement and exercise, and timing your meals to allow your gut to maintain a healthy cleaning schedule are all steps you can take to manage your symptoms.
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Herbal antimicrobials: For individuals who cannot tolerate pharmaceutical antibiotics some types of herbal antimicrobials like berberine (to use against hydrogen-producing bacteria), oregano oil (an all-purpose anti-microbial), or allicin from garlic extract (to use against methane-producing archaea) may prove effective. However, there is very little scientifically validated data on these types of herbal treatment options.
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Probiotics: While probiotics have become a popular topic in conversation and in the media, their effectiveness in treatment of many gut health conditions including SIBO, IMO, and ISO has not been well established. Additionally, the large variation in the probiotics available today–all with different microbial strains, inconsistent dose sizes, and varying delivery methods–means that there is very little conclusive evidence suggesting exactly how a patient will be affected by any one specific probiotic product. And it is possible that the use of probiotics could even worsen your symptoms. For these reasons, many prominent GI experts exercise caution in recommending probiotics as a standard treatment for these conditions.
As is usually the case when addressing medical conditions, no one course of management or combination of therapies can be universally applied to all patients in a population. If you’ve been diagnosed with SIBO, IMO, or ISO, or you are experiencing some of the symptoms mentioned in this article, it is vital for you to consult with your healthcare provider(s) to assess your condition, investigate possible causes, and explore which treatment and management approach will be most effective for you.
