IBS, SIBO (Small Intestinal Bacterial Overgrowth), or Both? 3 Things to Know

Bloating—that uncomfortable, sometimes painful, feeling of your belly being full and tight—is something many people experience from time to time, especially after a big, carbohydrate-rich meal.

But many health conditions can cause bloating—from common ones, like irritable bowel syndrome (IBS), to those you may never have heard of, such as SIBO (small intestinal bacterial overgrowth).

A healthy digestive system contains bacteria—the small intestine has lower levels of bacteria than the large intestine (colon). In people with SIBO, however, this balance shifts considerably, and excess bacteria in the small intestine leads to gastrointestinal (GI) symptoms.

“Although uncommon to most people, SIBO is one of the more common conditions GI specialists think about when patients have bloating and changes in their bowel habits,” says Jill Deutsch, MD, a Yale Medicine gastroenterologist. “SIBO can cause diarrhea, and some types of bacterial overgrowth can lead to constipation. Less commonly, individuals have abdominal pain or discomfort as well.”

Much about SIBO is poorly understood, including how many people are affected by it, what causes it, how to best test for it, and how to treat it without recurrence. But as researchers have learned more about the gut microbiome (the microorganisms that live in the GI tract and support digestion and immune defense), they have started to focus on connections between SIBO and IBS—a chronic condition with symptoms similar to SIBO, including changes in bowel habits, like diarrhea and constipation.

“IBS used to be a catch-all diagnosis, but now we’re seeing IBS and SIBO as separate, even though the treatments for both can be similar,” Dr. Deutsch says. “But it can be really challenging to differentiate SIBO from IBS as the symptoms overlap. The big difference is that IBS tends to be more pain-predominant, whereas a SIBO diagnosis tends to be more bloating-predominant.”

Because the excess bacteria in the small intestine can eat up nutrients, in severe cases, this leads to nutritional deficiencies, including in iron, vitamin B12, and vitamin D (among other fat-soluble vitamins). Usually, however, such deficiencies are mild and hard to detect. It can also be hard to differentiate SIBO from celiac disease, a type of autoimmune condition that affects the lining of the digestive tract and causes abdominal pain, weight loss, bloating, and diarrhea.

Adding to the confusion, other diseases like scleroderma can cause SIBO, and conditions such as IBS and Crohn’s disease (a form of inflammatory bowel disease) can also co-exist with SIBO, so it can be difficult to tell which came first. Symptoms can also vary greatly, Dr. Deutsch notes.

“There are many individuals walking around with SIBO who have no idea because either they're not bothered by the symptoms or the symptoms aren’t significant enough to bring to the attention of a provider,” Dr. Deutsch says. “Other individuals, though, are extremely bothered by the symptoms. And some people are more predisposed to being sensitive to this—as well as to specific food triggers, like carbohydrate-laden meals, that worsen symptoms.”

Below, we talk more with Dr. Deutsch about SIBO, including testing and treatment options.

Moving food through your digestive system requires a complex set of wave-like, involuntary contractions and relaxations of the muscles in your esophagus, stomach, and intestine. This process is called peristalsis, and it allows your body to break down food for digestion, absorb nutrients, and clear out bacteria and waste products. Steady peristalsis is important for maintaining a proper balance of bacteria in the digestive system.

But certain GI conditions can slow down peristalsis, causing food to pool in the digestive tract and leading to bacterial overgrowth and, thus, SIBO. Other conditions, including diabetes and scleroderma, can similarly cause decreased movement, or motility, in the small intestine. And surgeries that create pouches or 'blind loops’ in the small intestine (such as bariatric procedures) can also cause excess bacteria to grow there.

SIBO may also be associated with weak immune responses in the gut due to acid suppression caused by surgery or medications (like proton pump inhibitors) and various immunodeficiency syndromes.

There is disagreement among medical professionals about the best way to test for SIBO because of the limitations of various methods for diagnosis.

For one, the small intestine is difficult to reach. An upper endoscopy, which involves threading a long, flexible tube down the throat and esophagus, only reaches the top part of the small intestine. A colonoscopy, which involves threading a tube through the anus, rectum, and colon, only reaches the bottom of the small intestine.

Other testing methods are invasive and costly, including one that requires obtaining a bacterial culture. There is also a breath test, which is more commonly used but has its own limitations when it comes to accuracy and ease, Dr. Deutsch says.

The test measures the levels of hydrogen and methane in your breath. These gases are produced in the gut and are uniquely related to bacterial fermentation. The test involves fasting for 12 hours at night and then drinking a sugar solution of glucose or lactulose. You’ll then be asked to breathe into a machine for analysis every 15 to 20 minutes for three hours.

“Unfortunately, the data shows that the diagnostic breath tests are not great when we talk about sensitivity [the ability to identify who has a condition] and specificity [the ability to identify who does not have a condition], and it’s a three-hour-long, relatively involved test,” Dr. Deutsch says. “As a provider who sees this diagnosis quite frequently, I treat based on symptoms because the treatment is fairly safe, and if people don’t improve, then I reach to the diagnostic testing and start thinking outside the box and really question whether it’s truly SIBO.”

Antibiotics are most commonly used to treat the bacterial overgrowth responsible for SIBO. The most well-studied treatment for the condition is an antibiotic called rifaximin, Dr. Deutsch says.

“It’s nonabsorbed, meaning it acts locally in the GI tract so that it has minimal systemic, or whole-body, absorption. It’s not going to treat your tooth infection or toenail infection,” Dr. Deutsch says. “That was the reason it was chosen; it is fairly safe to use and because, unfortunately, SIBO can come back. Many of those predisposing conditions, like scleroderma, for example, don't have cures. Some have medications that can halt or slow down disease progression, but once it's there, it's there. So, there's not much we can do to prevent SIBO from returning.”

Most patients require a 14-day course of rifaximin, taken as a pill, and it can be used three or four times in one year, Dr. Deutsch says. However, rifaximin can be expensive and while it is approved by the Food and Drug Administration (FDA) to treat IBS, it is not approved for SIBO, which means it is prescribed off-label.

While systemically absorbed antibiotics can be used for SIBO, none are FDA-approved for it, and they can introduce another challenge. “I tend to be cautious with the use of those antibiotics, especially if they need to be reused repeatedly, because I don't want to breed multidrug-resistant bacteria,” Dr. Deutsch says. “Still, the efficacy of rifaximin is not that good—about 61% to 78%, whereas other systemic antibiotics like bactrim are 95% effective. It begs the question: Why don't you treat with systemic antibiotics if the efficacy is better than treating the condition multiple times with a less effective antibiotic? We don't want to use a systemic antibiotic unless we need to, in service of reducing the chances of creating antibiotic-resistant bacteria. But if rifaximin is ineffective, we’ll need to use a systemic one, such as bactrim,” she says.

As for diet, there are various ideas about how dietary changes can treat SIBO but very little scientific evidence to support any single dietary approach. However, it is logical to presume that a diet often used for IBS, called low FODMAP, may help, Dr. Deutsch says. The FODMAP acronym refers to a group of carbohydrates (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) that are difficult to absorb/digest in the small intestine for the predisposed individual. Rather, these carbs are fermented by microbes in the colon, which causes the same GI concerns mentioned earlier.

Many foods contain high levels of FODMAPs and include certain dairy items (milk, yogurt, and ice cream), fruits (apples, mangoes, and watermelon), vegetables (onions, garlic, and asparagus), beans and lentils, nuts (cashews and pistachios), and sweeteners (honey, high-fructose corn syrup, and low-calorie sweeteners).

“The low FODMAP diet has a ton of good data to support its use for the treatment of IBS. Essentially, it is suggesting that these fermentable sugars or short-chain carbohydrates can cause inflammation in someone who is already susceptible to having issues with these foods,” Dr. Deutsch says. “As far as I’m aware, we don’t have great data to support low FODMAP for SIBO, but we can see why it makes sense to try.”

However, because a low FODMAP diet requires significant modifications to what someone eats, Dr. Deutsch says she only recommends it to patients who have recurrent SIBO symptoms or those who have not been able to achieve significant relief with antibiotics.

“Plus, I have them work under the guidance of a registered dietitian who is knowledgeable about low FODMAP as it’s challenging and not something that people should just do on their own,” Dr. Deutsch says.