One condition we commonly evaluate at our clinic is Small Intestinal Bacterial Overgrowth, or SIBO. SIBO is not a new disease, but our understanding of it has changed considerably over the past several decades. During medical school and residency (finished 8 and 5 years ago, respectively), Irritable Bowel Syndrome (IBS) was discussed often, but I could probably count on one hand how many times we discussed SIBO.

It’s not uncommon for patients to come to us after years of struggling, having never heard of SIBO. It simply isn’t something most regular providers think to look for. Since joining PHW, SIBO has become one of the most common conditions I see. And although it’s not the explanation for every digestive symptom, identifying and treating SIBO can be an important piece of the puzzle for the right patient.

What is SIBO?

SIBO is often less about “bad bacteria” and more about too much bacteria in the wrong place. Your digestive tract is home to trillions of microorganisms, and it’s normal for some bacteria to pass through the small intestine on the way to the large intestine. The problem starts when they stay and multiply in the small intestine instead of moving along. This overgrowth can interfere with how you break down and absorb food, and it can lead to gas, bloating, and other digestive symptoms.¹˒³

Your small intestine has several ways of protecting itself, including stomach acid and your immune defenses. Another is something called the migrating motor complex (MMC), which you can think of as the intestine’s housekeeping system. Between meals and overnight, rhythmic waves of muscle activity sweep leftover food, digestive fluids, and bacteria along toward the large intestine. This only happens while you’re fasting, and eating interrupts it. When this sweeping action is disrupted, SIBO becomes more likely.⁴˒⁵

A number of things can disrupt the MMC and the gut’s other defenses, including:¹˒²

• Infections like food poisoning or traveler’s diarrhea
• Abdominal Surgery
• Certain medications, such as long-term acid reducers or opioid pain medications
• Diabetes or Hypothyroidism
• Inflammatory bowel disease (Crohn’s Disease or Ulcerative Colitis)
• Conditions that slow movement through the gut, such as gastroparesis or scleroderma
• Scar tissue (adhesions) that affects how things move through the gut

SIBO and IBS

SIBO and Irritable Bowel Syndrome (IBS) can look remarkably similar. Both may cause bloating, abdominal pain, diarrhea, constipation, or alternating bowel habits. This overlap is one reason SIBO can often be missed.

Research suggests a meaningful connection between the two. A 2020 systematic review and meta-analysis of 25 case-control studies found that approximately 35.5% of people with IBS had a positive SIBO breath test,⁶ and a newer 2026 meta-analysis of 81 studies found SIBO in approximately 40.4% of people with IBS.⁷ In other words, SIBO may be present in a sizable share of patients diagnosed with IBS, though more research is needed to understand exactly how the two are related, a point that is also emphasized by the American Gastroenterological Association.²

Not every patient with IBS has SIBO. But SIBO is a common and potentially treatable contributor to IBS-type symptoms and deserves consideration, particularly when symptoms are persistent, severe, or accompanied by risk factors for bacterial overgrowth.

Symptoms

The most familiar symptoms are bloating, a swollen or distended belly, abdominal pain or discomfort, excess gas or belching, reflux, indigestion, nausea, diarrhea, and constipation.¹˒² I often hear patients describe a flatter stomach in the morning or while fasting, then bloating once they start eating and feeling worse as the day goes on. Another common pattern is bloating that’s worse with higher-fiber foods. Patients assume they’re doing something good for themselves by eating a salad, then feel worse (because, unfortunately, SIBO microbes really love fiber!).

The type of gas being produced can also shape symptoms. Hydrogen-dominant overgrowth is more often linked to diarrhea, while methane is more strongly linked to constipation. Fun fact: methane is produced by archaea (single-celled organisms that aren’t bacteria), so methane-dominant cases are more accurately called Intestinal Methanogen Overgrowth, or IMO.⁸ A third gas, hydrogen sulfide, is less well understood, but it can be linked to diarrhea and sometimes causes a “rotten egg” smell in gas. These patterns offer useful clues, but they aren’t absolute rules.⁸˒⁹

SIBO can also cause problems beyond the familiar digestive symptoms. In more significant or longstanding cases, the excess microbes compete for nutrients and interfere with how you break down and absorb food. Changes in how the body handles bile acids (which help digest fat) and damage to the surface of the intestinal lining can contribute to iron deficiency, trouble absorbing fat, and low levels of vitamins such as B12 and the fat-soluble vitamins A, D, and K.³˒¹⁰

There is also growing interest in how SIBO relates to inflammation in the gut and intestinal permeability, commonly called “leaky gut.” The intestinal lining isn’t just a passive tube. It’s an active barrier that controls what passes between the contents of the intestine and the bloodstream and immune system. When this barrier is disrupted, permeability can increase. That has been associated with inflammatory and autoimmune conditions, and researchers are still working out how the gut microbiome, barrier health, and immune activity throughout the body are connected.¹¹˒¹²

But it’s important not to overstate what we know. SIBO has not been established as a direct cause of autoimmune disease or food allergy. The links between microbial overgrowth, intestinal permeability, food sensitivities, and body-wide inflammation are biologically plausible and an active area of research, but they’re better thought of as potentially interconnected processes than a simple cause-and-effect chain.

Testing

The most common test for SIBO is a hydrogen and methane breath test, which measures gases in your breath. After a prescribed preparation diet and fasting period, you drink a measured sugar solution. If microbes are present in the small intestine, they ferment the sugar and release hydrogen or methane gas, which is absorbed into the bloodstream and exhaled. Breath samples are collected at regular intervals over several hours, and the timing of the gas rise helps show where the microbes are. An early rise suggests they’re in the small intestine, where they don’t belong, rather than in the large intestine, where they do.⁸˒¹³

Testing isn’t perfect, however. The preparation, the way the test is performed, how quickly food moves through your gut, and how the results are interpreted can all affect the outcome. This is one reason SIBO remains an evolving area of gastroenterology.²˒¹³

Treatment

There are various treatment options, and no single treatment is right for everyone. In general, our approach has three goals:

• Reduce or eliminate the overgrowth.
• Improve symptoms and nutrition.
• Identify and address the underlying cause to reduce the chance of recurrence.

Rifaximin (Xifaxan) is an antibiotic that stays mostly in the gut rather than being absorbed into the bloodstream, and it is commonly used to treat SIBO.¹˒² It has particularly strong evidence for IBS with diarrhea.¹⁴ In SIBO studies, the rate of clearing the overgrowth on follow-up breath tests varies from patient to patient. That is another reason treatment should be individualized rather than seen as “take an antibiotic and you’re done.”¹˒¹⁵

Some patients prefer, or may be good candidates for, botanical or herbal antimicrobial therapy. Commonly used products contain herbs such as berberine, oregano, neem, and allicin, among others. One frequently cited 2014 study compared herbal therapy with rifaximin and found similar rates of negative follow-up breath tests.¹⁶ Controlled trials of botanicals are scarce, so this remains some of the best available evidence.

An elemental diet takes a very different approach. Instead of using something to kill the microbes, it provides nutrition already broken down into easily absorbed components, leaving very little undigested food to feed the overgrowth. In essence, it fully nourishes the patient while starving the overgrowth. In a 2004 study of IBS patients with abnormal lactulose breath tests, a two-week exclusive elemental diet normalized the breath test in 80% of participants by day 15, rising to 85% among those who continued to 21 days.¹⁷ It can be difficult to follow, relatively costly, and nutritionally and socially challenging, so it isn’t necessarily a first choice for every patient.

The low-FODMAP diet is one of the most useful tools we have for managing IBS symptoms, and the American College of Gastroenterology recommends a limited trial of it to improve overall IBS symptoms.¹⁸ FODMAPs are fermentable carbohydrates that intestinal microbes feed on, which contributes to gas and pulls extra water into the intestine. Reducing them can substantially ease bloating, abdominal pain, and changes in bowel habits for many people. But a low-FODMAP diet generally does not eradicate SIBO. It is primarily a symptom-management strategy. Ideally, it is a temporary tool rather than a permanent list of foods to fear. Once symptoms are controlled, foods should generally be reintroduced as tolerated.

We try to set realistic expectations early. SIBO treatment is often a long-term process, with ups and downs, changes of plan, and relapses. Some patients are lucky enough to have a single round of treatment and never see symptoms return. Unfortunately, that isn’t the case for most. It is usually better to start by viewing SIBO as a chronic condition to be managed rather than an infection that will be “cured” quickly or easily. If it turns out to be an easier case, that’s a pleasant surprise. If not, we’ve hopefully limited some of the disappointment and discouragement people can feel. Identifying and addressing the underlying cause is often the missing piece, and it gives us our best chance at long-term success.

The Root Cause and the Reoffender

This may be the most important part of treatment. The goal is not simply to “kill bacteria.” It is to restore a healthier intestinal environment. If we reduce the bacterial overgrowth but never address why it developed, those persisting environmental conditions may allow it to return. Recurrence of SIBO is unfortunately all too common. In one study of 80 patients whose SIBO initially normalized after Rifaximin treatment, patients experienced rates of recurrence of 12.6% at 3 months, 27.5% at 6 months and 43.7% at 9 months.¹⁹

Many of the underlying contributors to SIBO, and thus to its recurrence, relate to negative impacts on the gut’s immune defenses, especially intestinal motility. The MMC functions primarily during fasting, which is one reason some SIBO treatment approaches emphasize avoiding constant grazing/snacking, and allowing reasonable periods between meals. Many sources commonly recommend spacing meals by approximately 4–5 hours and allowing an overnight fasting period.²⁰

For patients with documented or suspected motility problems, a clinician may also consider a prokinetic agent, which is a medication or botanical approach intended to support gastrointestinal motility and the MMC. Small retrospective studies have suggested that motility-directed treatment may extend the time before recurrence, although this area also still needs better-quality research.²¹

This doesn’t mean that everyone with SIBO will have a chronic problem. It means that treating the underlying physiology is often at least as important as treating the overgrowth itself.

The Bottom Line

There is no single approach that magically repairs the intestinal lining. It is usually less about finding the “right” supplement or food, and more about creating conditions in which it can recover. In practice, supporting intestinal recovery means addressing what contributed to the problem, correcting nutrient deficiencies, supporting healthy gut movement, and using targeted nutritional or botanical support when appropriate. And it takes time, an often underappreciated key ingredient.

SIBO is a condition that sits at the intersection of digestion, motility, nutrition, and microbiome. It is common enough to deserve consideration, but complex enough that it should not become a catch-all explanation for every digestive complaint. When SIBO is suspected, the goal should be more than simply getting a positive test to turn negative. We want to understand why the overgrowth developed, treat it appropriately, restore normal digestive function, and reduce the chances that it comes back. For the right patient, that approach can turn a frustrating collection of symptoms into something much more understandable and treatable.