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What is SIBO (Small Intestinal Bacterial Overgrowth)?

SIBO, or Small Intestinal Bacterial Overgrowth, is a digestive disorder caused by an excessive growth of bacteria in the small intestine—bacteria that don’t usually reside in this part of the gut. It’s relatively common, affecting around 34% of people with gastrointestinal complaints, and it can significantly interfere with digestion and nutrient absorption. [1]

Symptoms are often non-specific and mimic those of other digestive conditions, which is why SIBO is frequently misdiagnosed or diagnosed late [2]. If left untreated, it can lead to serious complications, including long-term issues like malnutrition and vitamin deficiencies. That’s why early, accurate diagnosis and proper treatment are essential.

Symptoms of SIBO

SIBO symptoms vary from person to person but mainly affect the digestive system. The type and location of bacterial overgrowth influence the severity and nature of symptoms. Common complaints include bloating, loss of appetite, nausea, excess gas, altered bowel habits, a feeling of fullness after eating, unintentional weight loss, and malnutrition. Many of these symptoms stem from the fermentation of partially digested carbohydrates, which produces gases (hydrogen, methane) and acids. Gases can cause bloating, cramps, and constipation, while acids may irritate the intestinal lining, resulting in diarrhea. These effects can significantly impact quality of life and lead to further digestive problems. [3]

SIBO can also trigger extraintestinal symptoms. Because the digestive tract is closely linked to both the hormonal and nervous systems, an imbalance in gut bacteria may contribute to skin issues, anxiety, and more. [4]

Because these symptoms can also be caused by other gastrointestinal diseases, it’s important to determine whether SIBO is the underlying cause. Persistent diarrhea, rapid unexplained weight loss, or severe abdominal pain lasting more than a few days should prompt a visit to a doctor. [5]

Figure 1. SIBO symptoms vary from person to person but mainly affect the digestive system

If untreated, SIBO can cause a range of health issues. Byproducts from bacterial overgrowth can damage the intestinal lining, hindering the absorption of carbohydrates and proteins. Certain bacteria also degrade bile acids, impairing fat digestion and leading to diarrhea. In turn, poor fat absorption disrupts the uptake of fat-soluble vitamins such as A, E, and K as well as vitamin D. [3]

SIBO may also lead to vitamin B12 deficiency, as some bacteria consume large amounts of it. B12 is crucial for nervous system health, red blood cell production, and histamine breakdown. Deficiency can cause fatigue, weakness, and numbness. Hydrogen-producing bacteria are more often linked to B12 deficiency, while some methane-producing species may even synthesize B12 [6–7]. Additionally, SIBO can cause electrolyte imbalances, including chronic calcium deficiency, which can contribute to osteoporosis. [5]

Types of SIBO

SIBO is classified based on the dominant type of gas produced by the overgrown bacteria in the small intestine. Identifying the specific type is important, as symptoms and treatment options can vary accordingly. [8–9]

1. Hydrogen-dominant SIBO

This is the most common form, accounting for roughly 60% of cases. It’s caused by an overgrowth of hydrogen-producing bacteria, such as Escherichia coli and Klebsiella pneumoniae. Typical symptoms include diarrhea, bloating, and abdominal cramps. A common trigger is a disrupted gut microbiome, often due to prior antibiotic use. Diagnosis is usually confirmed through a hydrogen breath test.

2. Methane-dominant SIBO

In this type, bacteria in the small intestine produce methane—primarily by species like Methanobrevibacter smithii. Methane-dominant SIBO is often linked to reduced intestinal motility and constipation. Diagnosis typically involves a methane breath test using lactulose or glucose; however, this test is not currently available in all countries.

3. Mixed-type SIBO

This variant involves an overgrowth of both hydrogen- and methane-producing bacteria.

4. Hydrogen sulfide-dominant SIBO

In this form, bacteria use hydrogen to produce hydrogen sulfide, a gas with a distinctive sulfurous odor. In excess, hydrogen sulfide can relax smooth muscles and trigger inflammation. This subtype has been linked to various gastrointestinal conditions, including irritable bowel syndrome (IBS), leaky gut, and inflammatory bowel diseases. Known hydrogen sulfide-producing species include Citrobacter, Clostridium, Collinsella, Desulfovibrio, Escherichia, Enterobacter, Fusobacterium, Klebsiella, Prevotella, and Proteus.

5. SIFO (Small Intestinal Fungal Overgrowth)

SIFO is a condition where fungi overgrow in the small intestine, producing symptoms similar to SIBO.

Diagnosing SIBO: understanding the options

Diagnosing SIBO can be challenging due to its non-specific symptoms, which often resemble those of other gastrointestinal disorders. Additionally, the small intestine is anatomically difficult to access using conventional diagnostic tools like endoscopy. When a patient’s symptoms and medical history suggest SIBO, the most straightforward and non-invasive diagnostic method is a breath test. This test can confirm the diagnosis, determine the severity of bacterial overgrowth, and identify whether hydrogen- or methane-producing bacteria are dominant.

Breath tests

In SIBO, bacteria typically found in the large intestine begin to ferment carbohydrates in the small intestine, producing excess gas. The most common diagnostic tool is the hydrogen breath test, which detects hydrogen gas that enters the bloodstream and is then exhaled through the lungs. This early rise in hydrogen levels indicates bacterial overgrowth. Breath tests are non-invasive, cost-effective alternatives to endoscopic sampling. [10]

A breath test is considered positive for SIBO if hydrogen levels rise by more than 20 parts per million (ppm) above baseline within 90 minutes, or if methane levels exceed 10 ppm at any point within a two-hour window. [11]

Other Diagnostic Methods

• Blood tests: Used to evaluate vitamin levels, protein status, and markers of inflammation.
• Stool analysis: Helps detect undigested nutrients (fats, proteins, carbohydrates), bile acid imbalances, inflammation, and infections. Stool-based genome testing can also assess the gut microbiome’s composition. While this doesn’t specify the exact location of the bacteria, the presence of species typically found in the small intestine may indicate ileocecal valve dysfunction.
• Imaging studies: Useful for identifying anatomical or pathological changes that could promote or sustain SIBO.
• Small bowel aspirate and culture: This endoscopic procedure involves collecting a fluid sample from the upper small intestine for microbiological analysis. [12]

It’s important to understand that diagnosing SIBO often requires a combination of tests. There are currently no universally accepted thresholds for either breath tests or aspirates, which can make the diagnosis more difficult in borderline or unclear cases.

Development of SIBO

SIBO can develop as a result of motility, anatomical, immune, nervous system, metabolic, and other systemic disorders. Under normal conditions, the small intestine has several defense mechanisms to prevent bacterial overgrowth. These include stomach acid and bile, which destroy bacteria; peristalsis, which moves contents through the digestive tract; the ileocecal valve, which prevents backflow of bacteria from the large intestine; and secretory IgA, a key antibody that supports gut immunity. When any of these mechanisms are impaired, the risk of developing SIBO increases. [13]

Figure 2. SIBO can develop as a result of motility, anatomical, immune, nervous system, metabolic, and other systemic disorders

The role of stomach acid, bile, and the pancreas

Stomach acid and bile are critical for controlling the spread of bacteria through the gastrointestinal tract [13]. When stomach acid is low, protein digestion becomes insufficient, creating conditions favorable for bacterial growth. Low acid levels may be caused by Helicobacter pylori infection, acid-suppressing medications (e.g., proton pump inhibitors), surgery, or chronic stress. [14]

Bile duct or gallbladder dysfunction is also linked to SIBO. Impaired bile flow reduces its antimicrobial activity, increasing the risk of bacterial overgrowth. Furthermore, SIBO itself can worsen bile-related issues: bacteria in the small intestine encounter bile acids too early and degrade them prematurely—normally, this breakdown would occur in the large intestine. As a result, bile acids lose functionality, fat digestion is impaired, and absorption of fat-soluble vitamins suffers. [15]

The pancreas contributes by producing enzymes that help digest proteins. When pancreatic function is compromised—such as in chronic pancreatitis—protein digestion falters, promoting overgrowth in the small intestine and increasing the risk of SIBO. [16]

Disturbances in intestinal motility

The migrating motor complex (MMC) is a special type of peristalsis that occurs during fasting. Every 90–120 minutes, rhythmic contractions sweep through the stomach and small intestine to clear residual food and bacteria. When this system is disrupted, food remains in the small intestine too long, encouraging bacterial proliferation and even allowing colonic bacteria to migrate upward.

SIBO is often associated with conditions that impair gut motility, including IBS, use of narcotic medications, radiation enteritis, hypothyroidism, diabetes, and scleroderma. [13]

Anatomical factors

Proper function of the ileocecal valve (which separates the small and large intestine) and the ileum is essential for preventing backflow of large intestinal bacteria into the small intestine. Structural abnormalities like small intestinal diverticulosis, strictures, surgical adhesions, bariatric surgeries, or intestinal resections can all increase the likelihood of SIBO. [17]

The role of the immune system

Secretory IgA (sIgA) is a key antibody that helps control microbial populations in the gut and supports intestinal immunity. Immunodeficiencies—such as AIDS, common variable immunodeficiency, or selective IgA deficiency—are associated with an increased risk of SIBO.

The role of stress

The autonomic nervous system —responsible for regulating essential functions like breathing, heart rate, and digestion—has two branches: the sympathetic (“fight or flight”) and parasympathetic (“rest and digest”) systems. These interact closely with the enteric nervous system, which governs digestion. Chronic stress disrupts this balance, reducing digestive secretions, slowing motility, increasing visceral sensitivity, and impairing mucosal healing. It also increases intestinal permeability. [18]

The communication between the brain and gut is bi-directional. Chronic gut disturbances can, in turn, increase stress via the gut-brain axis. This feedback loop plays a role in many gastrointestinal conditions, including IBD, IBS, food intolerances, and peptic ulcers. [19]

In SIBO, dysfunction of the central stress response—specifically the hypothalamic-pituitary-adrenal (HPA) axis—can promote bacterial overgrowth in several ways. Stress hormones produced by the HPA axis can encourage the growth of harmful bacteria and weaken the immune system [20]. Additionally, stress inhibits the migrating motor complex, disrupting the body’s ability to clear bacteria from the small intestine [21]. Stress also reduces levels of sIgA, weakening mucosal immunity. In sum, HPA axis dysfunction contributes to impaired motility, weakened immunity, and bacterial overgrowth. [22]

SIBO and metabolic disorders

All living organisms absorb substances from their environment, break them down, convert them into energy, store them, and eliminate what remains. When these metabolic processes are disrupted, it can lead to chronic diseases such as high blood pressure, obesity, and diabetes. These conditions are often linked with low-grade, chronic inflammation—also known as “silent inflammation”—and typically involve alterations in the gut microbiome. In individuals with obesity, the balance of gut bacteria often shifts toward a higher ratio of Firmicutes compared to Bacteroides. This dysbiosis leads to more efficient calorie extraction from food and increased production of short-chain fatty acids. These, in turn, promote inflammation by releasing endotoxins that increase intestinal permeability. This creates a vicious cycle that links obesity with SIBO [23]. Dysbiosis is common not only in obese individuals but also in those with metabolic syndrome.

Gastrointestinal issues are also frequent in people with diabetes. Both type 1 and type 2 diabetics have a significantly higher risk of developing SIBO. Diabetic complications—such as autonomic neuropathy and persistently high blood sugar—can impair intestinal motility, providing favorable conditions for bacterial overgrowth. [23]

SIBO and IBS

SIBO is highly prevalent among individuals with irritable bowel syndrome (IBS). One study found that 157 out of 202 IBS patients (about 75%) also had SIBO [24]. It appears to be more closely associated with constipation-predominant IBS than with the diarrhea-predominant form [23]. Both SIBO and IBS activate the immune system, increasing levels of pro-inflammatory cytokines in the intestinal lining and contributing to increased gut permeability. Despite these similarities, treatment strategies for the two conditions may differ and should be tailored to the individual.

Treatments of SIBO

Managing SIBO requires a comprehensive, multi-layered approach. The main goals are to eliminate bacterial overgrowth in the small intestine, address any underlying causes and complications, and prevent recurrence.

Figure 3. Managing SIBO requires a comprehensive, multi-layered approach

Antibiotic therapy

Standard medical treatment typically begins with a course of antibiotics—either a single agent or a combination—targeted at reducing the bacterial load [5]. Because various bacterial strains may coexist, therapy must often be tailored to the individual [15]. Unfortunately, current research offers limited guidance on which antibiotics to use, at what dose, or for how long, resulting in a wide range of treatment practices [25]. A short course of antibiotics can significantly reduce pathogenic bacteria, but relapse is common. In some cases, long-term treatment may be necessary. One key concern is that antibiotics may also kill beneficial gut bacteria, potentially worsening gut imbalance.

Symptom management

Several treatments are available to help relieve the symptoms of SIBO. These include medications for bloating and abdominal pain, laxatives for constipation, and prokinetics to stimulate gut motility. Antidiarrheal agents may offer short-term relief for diarrhea. [13]

Ensuring proper production of stomach acid and digestive enzymes is also critical. When gastric acid or pancreatic enzymes are deficient, supplementation may be recommended.

Elimination diets

Dietary interventions play a central role in managing SIBO. Elimination diets—such as the Specific Carbohydrate Diet (SCD) and the low-FODMAP diet—limit fermentable carbohydrates (FODMAPs: fermentable oligosaccharides, disaccharides, monosaccharides, and polyols). These carbohydrates are poorly absorbed and easily fermented by gut bacteria. Reducing FODMAP intake can improve nutrient absorption and reduce bacterial overgrowth [26]. One study showed that people on a low-FODMAP diet experienced symptom relief, likely due to the diet’s manageability and reduced fermentation. [16], [27]

Elemental diet

In more severe cases—especially when antibiotics or elimination diets fail—doctors may recommend an elemental diet. This is a medical-grade, liquid diet that delivers nutrients in their most easily absorbed, pre-digested form.

An elemental diet can be used alongside antibiotics or as a standalone treatment, especially for patients who cannot tolerate antibiotics. It helps reduce food sources for bacteria while supporting nutrient absorption in the small intestine. However, this approach is highly restrictive and may cause side effects like nausea, abdominal discomfort, and diarrhea. It can also raise blood sugar levels, so it must be used under strict medical supervision in people with diabetes or kidney disease. [16]

Natural therapies and antimicrobial herbs

Addressing nutrient deficiencies is another critical part of SIBO treatment. Many individuals with SIBO experience malabsorption, leading to vitamin and mineral deficiencies. Replenishing these nutrients and supporting healthy weight gain are important goals of care.

The use of antimicrobial herbs in SIBO treatment is gaining recognition. A study at Johns Hopkins Hospital compared a targeted antibiotic to a concentrated herbal regimen in newly diagnosed SIBO patients over four weeks. Some herbal protocols were found to be as effective as antibiotics, with fewer side effects. [28–29]

Several herbs are known for their antimicrobial properties. Oregano (Origanum vulgare), for instance, directly kills or strongly inhibits the growth of intestinal microbes. Oregano oil also offers additional benefits, such as inducing apoptosis (programmed cell death) in human colon cancer cells. Thyme (Thymus vulgaris) exhibits broad-spectrum antibacterial activity. White wormwood (Artemisia absinthium) possesses significant antimicrobial and anti-inflammatory effects—an important aspect in the pathogenesis of SIBO—and has been successfully used to reduce intestinal inflammation. Red thyme (Thymus coccineus) essential oil inhibits the growth of certain Escherichia coli strains and Staphylococcus aureus. Indian barberry root extract (Berberis aristata), which contains berberine, demonstrates antimicrobial, anti-inflammatory, and anti-diarrhoeal effects. Field horsetail (Equisetum arvense) shows strong, broad-spectrum antimicrobial activity against a wide range of enteric microorganisms, including Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enteritidis, and fungi such as Aspergillus niger and Candida species. [30]

These herbs not only combat pathogens but may also support overall gut health. For example, lemon balm’s calming properties may benefit patients with IBS, while Coptis root supports both digestion and immune response.

Natural prokinetics like ginger, melatonin, curcumin, and peppermint oil may help restore healthy gut motility, preventing bacterial overgrowth and recurrence of SIBO.

Figure 4. Use of antimicrobial herbs in SIBO treatment is gaining recognition

Probiotics

Although data on probiotics in SIBO is limited, certain strains have shown benefits in related conditions like IBS, inflammatory bowel disease, and antibiotic-associated diarrhea. A 2014 study looked specifically at SIBO patients who received a three-week course of antibiotics. One group followed up with a synbiotic (a combination of prebiotics and probiotics) for six months, while the other did not. The synbiotic group experienced significant symptom improvement, including reduced pain, bloating, belching, and diarrhea. These findings suggest that synbiotics may enhance the effects of antibiotics and aid recovery. [31]

Though more research is needed, probiotics and prebiotics show promise in helping to restore microbial balance and reduce antibiotic side effects in SIBO treatment.

Fecal Microbiota Transplantation (FMT)

FMT involves transferring gut microbiota from a healthy donor to the patient’s intestinal tract, aiming to restore a balanced microbiome and suppress pathogenic bacteria. This emerging therapy is mainly used for severe or recurrent cases. Without proper donor screening, there’s a small risk of transmitting infections or other unwanted health conditions. [16]

Lifestyle and additional considerations

Lifestyle changes are a key part of managing SIBO. Chronic stress and dysfunction of the HPA axis are major contributors to both the development and recurrence of the condition. That’s why stress-reduction techniques—like aerobic exercise, meditation, massage, yoga, and healthy sleep routines—are highly recommended [32]. Ensuring sufficient intake of both macro- and micronutrients—possibly with supplementation—is also essential to support immune function and overall health. Altogether, these strategies contribute to a personalized, long-term restoration of a healthy gut microbiome.

Because treatment responses vary, SIBO management should involve a multidisciplinary team and active patient participation. All therapeutic decisions should ideally be made under professional medical guidance.For a personalized nutrition and lifestyle plan, consult with one of our specialists.

References

[1] I. Efremova et al., ‘Epidemiology of small intestinal bacterial overgrowth’, World J. Gastroenterol., vol. 29, no. 22, pp. 3400–3421, Jun. 2023, DOI: https://doi.org/10.3748/wjg.v29.i22.3400

[2] Y. K. Cho, J. Lee, and C. N. Paik, ‘Prevalence, risk factors, and treatment of small intestinal bacterial overgrowth in children’, Clin. Exp. Pediatr., vol. 66, no. 9, pp. 377–383, Aug. 2023, DOI: https://doi.org/10.3345/cep.2022.00969

[3] A. C. Dukowicz, B. E. Lacy, and G. M. Levine, ‘Small Intestinal Bacterial Overgrowth’, Gastroenterol. Hepatol., vol. 3, no. 2, pp. 112–122, Feb. 2007 https://pmc.ncbi.nlm.nih.gov/articles/PMC3099351/

[4] ‘SIBO – Bakterieovervækst i Tyndtarmen | Behandling af SIBO’ https://ibsklinikken.dk/behandlinger/hvad-er-sibo/

[5] ‘Small intestinal bacterial overgrowth (SIBO)-Small intestinal bacterial overgrowth (SIBO) – Symptoms & causes’, Mayo Clinic https://www.mayoclinic.org/diseases-conditions/small-intestinal-bacterial-overgrowth/symptoms-causes/syc-20370168