Small intestinal bacterial overgrowth (SIBO) is a condition in which excessive bacteria accumulate in the small intestine, leading to symptoms such as gastrointestinal pain, bloating, diarrhea, and nutrient malabsorption. Treatment focuses on eliminating the bacterial overgrowth and correcting nutritional deficiencies.

Antibiotics are the primary treatment, while certain dietary strategies and supplements may support recovery. In some cases, individuals may benefit from more advanced therapies like elemental diets or fecal microbiota transplant (FMT). Long-term management also includes addressing underlying causes such as motility disorders or chronic digestive conditions.

Antibiotic therapy

The initial approach to treating SIBO is typically the use of antibiotics that reduce or eliminate the excessive bacteria in the small intestine. Although no antibiotics are specifically approved by the FDA for treating SIBO, gastroenterologists commonly prescribe them off-label due to their effectiveness.

commonly prescribed antibiotics include:

  • Rifaximin (Xifaxan)

  • Neomycin

  • Ciprofloxacin (Cipro XR)

  • Metronidazole (Flagyl)

  • Tetracycline (Achromycin V)

  • Amoxicillin-clavulanate (Augmentin)

Off-label use refers to the prescription of a medication for a condition it isn’t officially approved to treat.

Rifaximin for hydrogen-predominant SIBO

Rifaximin is the most widely used antibiotic for SIBO, particularly for cases involving hydrogen-producing bacteria. A typical course lasts about two weeks. It is approved to treat traveler's diarrhea and IBS-related diarrhea, but is also effective in reducing bacterial overgrowth in the small intestine.

benefits of rifaximin:

  • Minimally absorbed into the bloodstream, limiting side effects

  • Targets bacteria in the small intestine without disturbing the colon

  • Generally well-tolerated by most individuals

contraindications:
Not recommended for individuals with liver disease, during pregnancy, or while breastfeeding.

Neomycin for methane-predominant SIBO

For individuals with methane-producing bacterial overgrowth, neomycin may be prescribed alongside rifaximin for improved effectiveness. Like rifaximin, neomycin primarily acts in the gut, reducing the growth of specific bacteria types.

caution:
Neomycin should not be used with blood thinners and may be unsafe for individuals with inflammatory bowel conditions, as these increase absorption and the risk of side effects.

Recurrent SIBO and retreatment

Nearly half of individuals treated for SIBO may experience a recurrence. This is more common among older adults, individuals using acid-suppressing medications, or those who have undergone an appendectomy. It’s also seen in conditions such as scleroderma and delayed gastric emptying (gastroparesis).

retreatment approach:

  • A second course of antibiotics may be prescribed if symptoms return within three months

  • If recurrence occurs after three months, a positive breath test may be required before administering another round of antibiotics

  • Avoiding unnecessary antibiotic use is important to prevent resistance and preserve gut microbiota

SIBO dietary strategies

Dietary changes can complement antibiotic treatment by reducing the food supply for gut bacteria, easing symptoms, and helping prevent recurrence.

Low-FODMAP diet

This elimination diet restricts fermentable carbohydrates (FODMAPs) that are poorly absorbed and commonly fermented by gut bacteria. Avoiding these carbohydrates may help reduce symptoms and bacterial growth in the small intestine.

foods high in FODMAPs to avoid:

  • Fruits: apples, pears, mangoes, dried fruits

  • Vegetables: garlic, onion, cabbage, cauliflower, asparagus

  • Dairy: milk, yogurt, cheese

  • Legumes: black beans, lentils, kidney beans

  • Nuts: cashews, pistachios

  • Grains: wheat bread, pasta, baked goods

  • Sweeteners: honey, high-fructose corn syrup, sugar alcohols

  • Drinks: apple juice, sweetened tea, beer

how it works:
The diet has two phases—elimination and reintroduction. Foods are removed for 2–6 weeks and then gradually reintroduced to identify individual triggers. While the low-FODMAP diet helps with symptom management, its long-term ability to eliminate SIBO is not yet conclusive.

Elemental diet

The elemental diet consists of a liquid formula containing pre-digested nutrients, which are easier for the small intestine to absorb. This diet reduces food residue that could feed bacterial overgrowth.

uses and benefits:

  • Often used alongside or in place of antibiotics

  • Supports nutrient absorption

  • May reduce symptoms in individuals with severe or persistent SIBO

limitations:

  • Difficult to adhere to due to taste and restriction

  • May cause side effects like nausea, bloating, or diarrhea

  • Not recommended for individuals with diabetes or kidney disease

Although small studies show promising results, larger trials are needed to confirm the diet’s effectiveness in managing SIBO.

Nutritional supplementation

SIBO can impair the body’s ability to absorb essential nutrients, resulting in various deficiencies. Managing these deficiencies is critical to improving symptoms and supporting overall health.

commonly deficient nutrients:

  • Thiamine (vitamin B1)

  • Niacin (vitamin B3)

  • Vitamin B12

  • Iron

  • Vitamins A, D, and E (fat-soluble)

fat malabsorption:
In some cases, individuals may experience steatorrhea (oily stools), indicating fat absorption issues. Additional supplementation or treatment may be needed.

Fecal microbiota transplant (FMT)

FMT involves transferring stool from a healthy donor into a recipient’s gut to restore a healthy microbial balance. It can be delivered via a colonoscopy, enema, or freeze-dried capsules.

current use:
Approved for treating C. difficile infections, but also being explored as a treatment for recurrent or severe SIBO, IBS, and inflammatory bowel disease.

early findings:
Preliminary studies have shown reductions in SIBO symptoms and increased microbial diversity after FMT. However, this remains an experimental approach and is generally reserved for chronic or relapsing cases.

possible risks:

  • Allergic reactions

  • Breathing issues

  • Infection or disease transmission from unscreened donors

  • Bleeding during procedures

Living with and managing SIBO

SIBO is usually manageable and does not typically result in long-term complications. However, in cases of severe or recurrent SIBO, patients may experience weight loss or malnutrition. For those with frequent recurrences, providers may suggest rotating antibiotic treatments every two weeks or monthly, sometimes switching antibiotics every few months.

persistent symptoms:
If symptoms do not improve with treatment, further investigation into other conditions such as Crohn’s disease, ulcerative colitis, or celiac disease may be necessary. These conditions can either mimic SIBO or contribute to bacterial overgrowth.

Treating the root cause

To improve treatment success and reduce recurrence, it's essential to address underlying issues that promote bacterial overgrowth.

common causes include:

  • Irritable bowel syndrome (IBS)

  • Chronic pancreatitis

  • Intestinal motility disorders

Proper evaluation and treatment of these conditions play a key role in the long-term management of SIBO.

Summary

SIBO is a condition caused by bacterial overgrowth in the small intestine, resulting in digestive symptoms and nutrient deficiencies. The cornerstone of treatment is antibiotics—especially rifaximin, often combined or rotated with others for recurrent cases. Dietary strategies like the low-FODMAP and elemental diets can support bacterial control and symptom relief.

Supplements may be needed to correct vitamin and mineral deficiencies. In severe or chronic cases, FMT is being explored as a potential treatment. Managing the underlying causes of SIBO is crucial to preventing relapse and ensuring long-term digestive health.