How Is SIBO Treated?
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Medically reviewed by Kumkum Sarkar Patel, MD
Small intestinal bacterial overgrowth, or SIBO, is bacteria overgrowth in the small intestine that causes gastrointestinal (GI) pain, diarrhea, bloating, and nutrient malabsorption.
SIBO is usually treated with antibiotics to stop bacterial overgrowth and dietary supplements to treat nutrient deficiencies. Some people with SIBO may also benefit from an elemental or low-FODMAP diet to avoid foods that trigger symptoms and reduce bacteria overgrowth.
A gastroenterologist—a provider specializing in treating digestive disorders—will oversee your SIBO treatment. Treatment aims to stop bacterial overgrowth to relieve and prevent symptoms. Antibiotic treatments are typically effective, but symptoms can keep returning. Long-term diet adjustments help manage bacteria levels and symptoms. SIBO is often caused by underlying conditions that also require treatment.
Antibiotics
SIBO is initially treated with antibiotics to kill excess bacteria in the small intestine. The U.S. Food and Drug Administration (FDA) has not approved any antibiotics to treat SIBO. A gastroenterologist will often prescribe off-label antibiotic treatments that help reduce and stop bacterial overgrowth, including:
Xifaxan (rifaximin)
Neomycin
Cipro XR (ciprofloxacin)
Flagyl (metronidazole)
Achromycin V (tetracycline)
Augmentin (amoxicillin-clavulanate)
Off-label simply means administering a drug for something it isn’t approved to treat.
Xifaxan
Xifaxan is the most common antibiotic used to treat SIBO. If SIBO is caused by hydrogen-predominant bacterial overgrowth, your provider will likely prescribe Xifaxan for about two weeks.
Xifaxan is FDA-approved to treat traveler's diarrhea and diarrhea due to irritable bowel syndrome (IBS). Unlike other antibiotics, research shows that Xifaxan can help kill bacteria overgrowth in the small intestine without reducing bacteria in the colon (large intestine).
The antibiotic is also not fully absorbed into the gut and bloodstream, which reduces side effects like nausea, bloating, diarrhea, and constipation. This effect also helps it target bacteria in the small intestine more directly.
Xifaxan is not considered safe if you have liver disease, are pregnant, or are breastfeeding.
Neomycin
If you have methane-predominant bacterial overgrowth, your provider may prescribe neomycin and Xifaxan together for two weeks. Neomycin helps kill harmful bacteria and suppresses bacterial growth. Like Xifaxan, it's not fully absorbed into the bloodstream, which helps it target bacteria in the small intestine.
Neomycin should not be combined with blood thinners like Coumadin (warfarin). It's also unsafe if you have inflammatory GI conditions like IBS and inflammatory bowel disease (IBD), as those conditions can increase antibiotic absorption and side effects.
Antibiotics for Recurrent SIBO
About 45% of people have recurrent SIBO after antibiotic treatment. This is more common in older adults, people who use proton pump inhibitors, and people who had their appendix removed (appendectomy). Recurrent SIBO also occurs in patients who have scleroderma (an autoimmune condition that thickens skin and other tissues) or gastroparesis (delayed stomach emptying).
You'll likely receive another round of antibiotics if SIBO symptoms return within three months. Your provider may also choose to use a different antibiotic. If symptoms return after three months, your healthcare provider usually won't give you another round of antibiotics unless you have a positive carbohydrate breath test to indicate you still have SIBO.
Antibiotic overuse can harm gut bacteria and make bacteria antibiotic-resistant, meaning they no longer respond to antibiotic treatment.
SIBO Diet
In addition to antibiotic treatment to stop bacterial overgrowth, following a SIBO diet may also help reduce bacteria overgrowth.
Low-FODMAP Diet
The low-FODMAP diet (low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet) is an elimination diet that removes carbohydrates called FODMAPs. FODMAPs are difficult for the digestive system to absorb, and bacteria like to feed on them. Reducing this type of carbohydrate may improve SIBO symptoms and nutrient absorption and reduce bacteria overgrowth.
While following the elimination phase of the diet, you'll avoid FODMAPs for about 2-6 weeks. Foods high in FODMAPs include:
Fruits like apples, peaches, cherries, pears, dried fruit, mangos, plums
Vegetables like asparagus, cabbage, cauliflower, Brussels sprouts, fennel, mushrooms, onion, garlic
Dairy products like milk, yogurt, and cheese
Legumes like black beans, lentils, kidney beans
Marinated and processed meats
Nuts like cashews and pistachios
Grain products like pasta, wheat bread, and baked goods
Sweeteners like honey, high-fructose corn syrup, and sugar alcohols (like sorbitol, mannitol, and xylitol)
Drinks like beer, sweetened teas, and apple juice
During the reintroduction phase, you'll add certain FODMAP foods—like fruits—for about three days to see if they trigger SIBO symptoms. Depending on how you tolerate certain foods, you may need to continue limiting certain high-FODMAP foods.
Research is inconclusive about whether the low-FODMAP diet can cure SIBO. Studies show that it offers people SIBO symptom relief, and it's easier to follow than more complicated, restrictive diets. However, most research on the low FODMAP diet focuses on treating IBS.
Elemental Diet
The elemental diet is a medical liquid diet that helps treat difficulty digesting food and absorbing nutrients. You'll drink a nutrient-dense liquid instead of typical meals. The nutrients in the liquid are in their "predigested" form (or elemental form) to help increase absorption.
The elemental diet is often used in addition to antibiotic treatment. It might be used alone if you can't tolerate antibiotics. Studies show that it helps the small intestine absorb nutrients while reducing food waste that bacteria like to feed on. When paired with antibiotics, this effect may help improve nutrient absorption and reduce bacteria overgrowth.
One small 2004 study included people with IBS and abnormal lactulose breath test (LBT)—a sign of SIBO. Results showed that 80% of participants had typical LBT levels after 14 days and 85% reached typical LBT levels after 21 days. However, this study only included 93 people. More research is needed.
Most people have difficulty sticking with the elemental diet because it's very restrictive, they don't like the taste of the liquid, or they experience side effects like abdominal pain, nausea, and diarrhea. The elemental diet may also increase blood sugar levels and is not considered safe for people with diabetes or kidney disease.
Supplements
SIBO treatment also involves treating any underlying nutrient deficiencies to improve SIBO symptoms. People with SIBO often have trouble absorbing:
Thiamine (Vitamin B1)
Niacin (Vitamin B3)
Fat-soluble vitamins like A, D, and E
Your healthcare provider may also have you take vitamin and mineral supplements to treat nutritional deficiencies caused by SIBO.
Fat Malabsorption
People with fat malabsorption—meaning the intestine can't properly absorb fat—will have steatorrhea (oily stool) in addition to other SIBO symptoms.
Fecal Microbiota Transplant
Fecal microbiota transplant (FMT) involves transplanting donor stool with healthy gut bacteria into the rectum (the lowest part of the colon) using a flexible tube. This may help restore beneficial bacteria and stop the overgrowth of harmful bacteria. A freeze-dried donor stool capsule may be ingested orally (by mouth) instead.
Currently, two FMT products are FDA-approved for treating C. difficile (C. diff), a bacterial infection that causes symptoms like diarrhea. FMT may also be used to treat SIBO, IBS, and IBD like Crohn's disease and ulcerative colitis. However, these are considered experimental, off-label treatments.
Using FMT to treat SIBO is a fairly new treatment method reserved for severe, recurrent cases. One 2021 study, which included 55 people with SIBO, found that those who took FMT capsules for four weeks had fewer SIBO symptoms and greater gut bacteria diversity. More research is needed.
FMT is generally considered a safe treatment. Possible side effects include:
Bleeding
Breathing issues
Allergic reactions to medications during FMT procedures.
In rare cases, FMT can increase your risk of disease from the donor due to improper screening, infection, and blood clots.
Living With and Managing SIBO
SIBO is often treatable with antibiotics and doesn't lead to long-term complications. In rare cases, severe recurrent SIBO can cause extreme weight loss and malnutrition. If you have recurrent SIBO and symptoms return more than four times a year, your gastroenterologist may suggest taking antibiotics for 5-10 days every two weeks or once a month. Your provider may also change your antibiotics every 2-3 months.
About 40% of people with SIBO-like symptoms are not cured with antibiotics. If you still have severe GI symptoms after several treatments, your provider may evaluate you for other intestinal conditions. SIBO symptoms are very similar to symptoms of IBD—including Crohn's disease and ulcerative colitis—and celiac disease. These conditions can also lead to SIBO.
Treating the underlying cause of bacteria overgrowth increases the success of treating and preventing recurrent SIBO. About 80-90% of SIBO cases are caused by IBS, intestinal motility disorders, or chronic pancreatitis (pancreas inflammation). If you have SIBO, your provider should also evaluate you for other underlying health conditions that can cause bacterial overgrowth.
A Quick Review
SIBO can typically be treated with antibiotics to kill bacterial overgrowth and dietary supplements to treat any SIBO-related nutrient deficiencies. Rifaximin is the most common off-label antibiotic used to treat SIBO, but your provider may combine or alternate antibiotics as needed. Diets like the elemental or low-FODMAP diet may also help reduce SIBO symptoms.
Fecal microbiota transplant (FMT) is a new option for severe cases, but it is still being studied and considered experimental. In most cases, SIBO can be effectively treated if the underlying cause—like IBS, IBD, or chronic pancreatitis—is also being treated. However, many people experience recurrent SIBO that may require multiple rounds of antibiotics to treat.
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