SIBO (small intestinal bacterial overgrowth) is an increase of bacteria, or the presence of bacteria in the wrong place, in the small intestine, where there are normally few. It can cause bloating, gas, diarrhea, constipation, reflux, fatigue and poor nutrient absorption. Symptoms overlap with irritable bowel, which is why diagnosis and treatment need follow-up.

In short

SIBO is an excess of bacteria in the small intestine, not an ordinary infection: it usually has an underlying cause.
There are three gas types: hydrogen, methane and hydrogen sulfide, linked to different symptoms.
The most used diagnostic is the breath test, which needs correct preparation.
Treating without fixing the cause raises the risk of relapse: the plan involves antimicrobials, food, motility and the underlying condition.

What happens in the gut

The small intestine is where most digestion and nutrient absorption takes place. When there are too many bacteria, they ferment food too early, produce gas, irritate the lining and interfere with the absorption of fats, vitamin B12, iron and fat-soluble vitamins.

Most common symptoms

Bloating and abdominal distension, gas, pain or discomfort, diarrhea, constipation, nausea, reflux, fatigue and, in more severe cases, weight loss, anemia and nutrient deficiencies.

Why it is confused with irritable bowel

Symptoms are very similar, and SIBO may be present in some people with IBS. Investigation helps tell the two apart, and they can coexist.

The three types of SIBO

Hydrogen

Produced by bacteria that ferment carbohydrates. Usually linked to diarrhea, gas and bloating.

Methane (IMO)

Produced by archaea, not bacteria, which led to the term “intestinal methanogen overgrowth” (IMO). Usually linked to constipation and bloating, and generally calls for combinations of antimicrobials.

Hydrogen sulfide

A gas that smells like rotten eggs, linked to diarrhea, pain and strong-smelling gas. It does not show up in traditional hydrogen and methane breath tests, and diagnosis depends on newer tests and clinical evaluation.

Why SIBO happens

The gut protects itself from excess bacteria with stomach acid, bile, enzymes, the immune system and, above all, the waves of movement that “sweep” the intestine between meals. When one of these mechanisms fails, bacteria can multiply.

Reduced gut motility: diabetes, hypothyroidism, scleroderma, gastroparesis and opioid use.
Abdominal and bariatric surgery, adhesions and anatomical changes, such as diverticula and narrowings.
Long-term use of proton pump inhibitors (omeprazole and similar), which lower stomach acid.
Celiac disease, Crohn's disease, chronic pancreatitis and other gastrointestinal diseases.
Previous gastroenteritis and infections, which can change how the gut works.
Aging and conditions that affect immunity.

SIBO is often the consequence of another problem. That is why investigating the cause is part of treatment: without it, symptoms tend to return.

How it is diagnosed

Diagnosis considers symptoms, history, risk factors and tests. The most used is the breath test with a substrate (lactulose or glucose), which measures hydrogen and methane in exhaled air over about 2 to 3 hours.

What the test shows

An early rise in hydrogen or high methane levels suggest overgrowth. The result must be interpreted along with symptoms, since the test is not perfect and can give false positives and false negatives.

Preparation is essential

It generally requires fasting for 8 to 12 hours, a diet low in fermentable foods the day before, and stopping antibiotics, laxatives and other medicines within time frames set by the lab and the doctor. Do not stop medicines on your own. Follow the lab's protocol.

Other investigations

Depending on symptoms, blood tests, celiac disease screening, thyroid assessment, blood glucose and other tests may be needed to investigate the cause and nutrient deficiencies.

There is also collection of small intestinal fluid by endoscopy, but it is a procedure that is rarely available and used in specific situations.

Treatment options

Treatment is individualized and led by the doctor, with nutritional support. There is no single recipe, and using medicines and herbal products without evaluation can get in the way.

Antibiotics

Rifaximin, which acts in the gut with little absorption, is the most studied option for hydrogen SIBO. In the methane type, another antimicrobial is usually added. The choice, dose and duration are medical decisions.

Herbal antimicrobials

Some, such as berberine, oregano oil and allicin, have been studied in small trials, with results close to those of antibiotics in some cases. Evidence is still limited, and safety, interactions and product quality should be assessed by a professional.

Specific diets

Low-FODMAP diets or other forms of restriction can relieve symptoms for a short time, but they do not remove the cause and should not go on for long. The elemental diet is used in selected cases, under supervision.

Probiotics

Results vary and depend on the strain. In some cases they may relieve symptoms, but in others they can worsen bloating. The choice should be individualized.

Prokinetics and motility

After treatment, medicines or measures that stimulate gut movement, and gaps of at least 4 to 5 hours between meals, help prevent relapse. This should be assessed individually.

Nutritional supplementation

When there is a deficiency, vitamin B12, iron, vitamin D and other nutrients may need to be replaced, based on tests.

Food during care

Food helps control symptoms and reduces what bacteria have to ferment, but it does not replace treating the cause.

Leave 4 to 5 hours between meals, without grazing all day, to give the gut's “cleaning movement” a chance.
Chew well and eat slowly.
Choose simple, minimally processed foods, with protein, well-tolerated vegetables and good-quality fats.
Temporarily and under guidance, reduce foods rich in FODMAPs, sugars and sweeteners such as sorbitol and xylitol.
Drink water throughout the day and avoid excess alcohol.
Reintroduce foods gradually, avoiding a restrictive diet for an indefinite period.

A very restrictive, prolonged diet can reduce microbiome diversity and cause deficiencies. It should be part of a plan with a start, goals and reassessment.

How to prevent relapses

Recurrence is common, especially when the underlying cause remains. Some measures help:

Treat or control associated conditions, such as diabetes, hypothyroidism and celiac disease.
Review long-term use of medicines that lower stomach acid, together with your doctor.
Keep gaps between meals and sleep at regular times.
Stay physically active and manage stress, which affect the gut.
Correct nutrient deficiencies and monitor symptoms.
Follow up with a professional, and repeat tests only when indicated.

Care for the symptoms and the cause

In the consultation, I assess symptoms, tests, history and routine to organize the investigation, food and nutritional deficiencies, together with your doctor, so that treatment is safe and relapse is less likely.

Book a consultation

Dra. Daniely Catharino TooleyClinical, functional and orthomolecular nutritionist · CRN3/6794

References (4)+

Pimentel et al. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol, 2020.
Rezaie et al. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. Am J Gastroenterol, 2017.
Chedid et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med, 2014.
Quigley et al. AGA Clinical Practice Update on Small Intestinal Bacterial Overgrowth: Expert Review. Gastroenterology, 2020.

Educational content for adults. This guidance does not replace an individual consultation, diagnosis or treatment.

SIBO: diagnosis and treatment