Edit concept Question Editor Create issue ticket

Small Intestinal Bacterial Overgrowth

Small Bowel Bacterial Overgrowth

Small intestinal bacterial overgrowth is described as the accumulation of a large number of bacteria in this organ, which should not normally be located in the structure. There are often underlying diseases and factors associated with the development of this condition.


The clinical picture is variable. Some patients will present with symptoms, while other will feature resemblance to IBS. According to studies that investigated the chief features of SIBO, there is a consequential sequence of diarrhea, abdominal pain, and then bloating.

Note that most studies did not use validated questionnaires to identify symptoms, therefore, the details are lacking.

An important aspect of the overall patient presentation is malabsorption and the resultant signs. Examples include weight loss and deficiencies in fat soluble vitamins and folate. Furthermore, nutritional deficiencies may occur due to the malabsorption of fat, carbohydrates, and protein. The symptoms associated are bloating, cramping, diarrhea, anorexia, and weight loss.

In patients with vitamin D deficiency, there are risks for the development of osteomalacia, hypocalcemia and osteoporosis. The latter is a known sequela of SIBO. Additionally, the lack of vitamin E may lead to neuropathy.

Vitamin B12 deficiency causes megaloblastic, macrocytic anemia and polyneuropathy. This vitamin deficiency likely results from the utilization of the vitamin by facultative Gram-negative aerobes and anaerobes.

Also, iron deficiency anemia may develop due to mucosal damage.

  • Intestinal motility disorders associated with diabetic neuropathy, systemic sclerosis, amyloidosis, hypothyroidism, and idiopathic intestinal pseudo-obstruction can also impair bacterial clearance.[merckmanuals.com]
  • Malnutrition Malabsorption Hypothyroidism Immunodeficiency The following potential underlying diseases are not amenable to treatment, but prevention of their progression may be therapeutic: Diabetic autonomic neuropathy Scleroderma Pseudoobstruction Amyloidosis[emedicine.medscape.com]
Abdominal Obesity
  • In multivariate analysis, the odds ratios of SIBO were 0.396 (P 0.018) for obesity and 0.482 (P 0.021) for abdominal obesity.[ncbi.nlm.nih.gov]
Sleep Apnea
  • We theorize that cytokine production produced by small intestinal bacterial overgrowth and obstructive sleep apnea may act as stimuli for ongoing CRPS symptoms.[ncbi.nlm.nih.gov]
Abdominal Pain
  • METHODS: In this study, 30 cases suffering from chronic abdominal pain or diarrhoea and with a positive hydrogen breath test were randomized in a double-blind manner into two groups: probiotic drug user and control group.[ncbi.nlm.nih.gov]
  • Abstract Irritable bowel syndrome (IBS) is a common condition characterized by abdominal pain or discomfort, bloating, and altered stool form and passage.[ncbi.nlm.nih.gov]
  • The patient, who declared to have always abstained from alcohol, was hospitalized for abdominal pain, belching and mental confusion. The laboratory findings showed the presence of ethanol in the blood.[ncbi.nlm.nih.gov]
  • OBJECTIVES: A potential link between small intestinal bacterial overgrowth (SIBO) and abdominal pain-related functional gastrointestinal disorders (AP-FGID) has been suggested by symptom similarities and by the reported prevalence of SIBO in children[ncbi.nlm.nih.gov]
  • METHODS: Patients who have undergone a lactulose or glucose hydrogen breath test to rule out small intestinal bacterial overgrowth (SIBO) for various clinical symptoms, including diarrhoea, weight loss, abdominal pain, cramping or bloating, were seen[ncbi.nlm.nih.gov]
  • A 64-year-old woman presented with heavy diarrhoea, nausea and weight loss accompanied by alopecia and dystrophic fingernails and toenails.[ncbi.nlm.nih.gov]
  • We also had patients complete a pretest symptom survey to evaluate nausea, bloating, constipation, diarrhea, belching, and flatulence.A total of 78 patients (69 females, 9 males, mean age of 48 years, mean BMI of 25.9) were evaluated.[ncbi.nlm.nih.gov]
  • Patients with bacterial overgrowth typically develop symptoms including nausea, bloating, vomiting, diarrhea, malnutrition, weight loss and malabsorption.[furtherfood.com]
  • A condition characterised by nausea, vomiting, bloating, flatulence, diarrhoea, and steatorrhoea linked to a relative increase in bacteria in GI content which over time may be result in malnutrition Diagnosis Jejunum aspirate with 105 bacteria/ml Risk[medical-dictionary.thefreedictionary.com]
  • Common symptoms of SIBO include: Gas and Bloating Abdominal Pain IBS type symptoms, including Diarrhea and Constipation or alternating between the two Heartburn and Nausea If you have had a Concussion or Traumatic Brain Injury in the past, suffer from[drbrandonspletzer.com]
Abdominal Distension
  • The most common symptom was abdominal distension (8/9, 88.9%), followed by abdominal discomfort (6/9, 66.7%). Rifaximin was prescribed to the nine patients with positive HBT, but two patients refused to take the medication.[ncbi.nlm.nih.gov]
  • Diagnostic testing with the XBT was performed based on a clinical suspicion for SIBO in patients with symptoms of bloating, abdominal pain, abdominal distension, weight loss, diarrhea, and/or constipation.[ncbi.nlm.nih.gov]
  • Abdominal distension. Malabsorption of fats. Food intolerances to lactose, gluten, caffeine, fructose, and others. Abdominal pain or cramping. Digestion problems like constipation. Irritable bowel syndrome or inflammatory bowel disease.[steptohealth.com]
  • The symptoms of bacterial overgrowth include nausea, flatus, [5] constipation, [6] bloating, abdominal distension, abdominal pain or discomfort, diarrhea, fatigue, and weakness. [7] SIBO also causes an increased permeability of the small intestine. [8[en.wikipedia.org]
  • Those with abdominal symptoms such as abdominal distension and abdominal pain 3. Abdominal simple X-ray examination recognizes small intestinal gas or recognizes intestinal fecal sign by CT examination 4.[upload.umin.ac.jp]
  • After adjusting for disease duration, SIBO was significantly associated with lower constipation and tenesmus severity scores, but worse scores across a range of "on"-medication motor assessments (accounting for 4.2-9.0% of the variance in motor scores[ncbi.nlm.nih.gov]
  • A 17-year-old woman, with a history of three operations on the upper gut in early life and intermittent diarrhoea, presented with a history of epistaxis and leg ecchymosis for the previous 3 months.[ncbi.nlm.nih.gov]
  • […] using the lactulose-hydrogen breath test; questionnaires of gastrointestinal symptoms and quality of life (PDQ-39); the Unified PD Rating Scale (UPDRS) including "on"-medication Part III (motor severity) score; and objective and quantitative measures of bradykinesia[ncbi.nlm.nih.gov]
  • Novel molecular techniques provide an exciting and challenging opportunity to explore the host-gut microbiota interaction.[ncbi.nlm.nih.gov]


The evaluation of the patient with a clinical picture suggestive of SIBO includes a thorough assessment of the medical and surgical history, a physical exam, and the following tests.

One investigation involves the proper assessment of the stomach and small bowel through gastroscopy and a biopsy. The findings may resemble those of celiac disease, which includes villous blunting, crypt hyperplasia, and increased lymphocytes in the lamina propria.

The gold standard test for SIBO is the identification of at least 105 bacteria per milliliter of jejunal aspirates, as the small intestine normally has less than 104 bacteria per milliliter. There is some doubt about the reliability of this test since SIBO can be patchy. Also, the findings may not be reproducible.

Another study is the D-xylose test, in which the patient drinks xylose, a sugar that is not digested by enzymes. After consumption, the D-xylose levels are measured in the blood and urine. The absence of the sugar indicates malabsorption.

Further investigations include breath tests that are designed to assess bacterial overgrowth. In the hydrogen breath test, the individual drinks glucose or lactulose, following a period of a 12 hour fast. Afterward, the hydrogen and methane levels are measured from the patient's expired breath. Similarly, the glycocholic acid breath test uses the bile acid for the detection of 14CO2, which is increased in cases of excessive bacterial growth. Note that these tests face questions regarding their reliability since there is a high rate of false positives.

Clinicians may implement a treatment trial to confirm the diagnosis in cases highly suggestive of SIBO. An improvement of symptoms indicates SIBO.


A complete blood count (CBC) and vitamin levels should be obtained to determine deficiencies and abnormalities associated with SIBO.

Pancreatic Calcification
  • Age, gender, body mass index (BMI), steatorrhoea, pain, analgesic use, pancreatic calcifications and use of pancreatic enzyme supplements had no relationship with the presence of SIBO.[ncbi.nlm.nih.gov]
Liver Biopsy
  • METHODS: Thirty-eight patients with NASH (age 37.5 years, range 20-54, 9, 24% female), diagnosed by ultrasonography, alanine aminotransferase 1.5 times normal and liver biopsy (in 27/38, 71%) and exclusion of other causes and 12 constipation-predominant[ncbi.nlm.nih.gov]


The treatment of SIBO should be directed at the etiology if possible, which may be an underlying disorder or a structural abnormality. The main therapeutic approaches are antibiotic use, probiotic therapy, and correction of nutritional deficiencies.


Therapy may consist of bacterial overgrowth correction with empiric antibiotics aimed at the treatment of aerobic and anaerobic enterobacteria. While there is no specific regimen, the options are metronidazole, ciprofloxacin, neomycin, norfloxacin, and doxycycline. Furthermore, one study demonstrated that more than 90% of strains in SIBO patients were eliminated by the combination of cefoxitin and amoxicillin–clavulanic acid. Additionally, ciprofloxacin exhibited strong activity in 70% of cases. Another drug, rifaximin, may be beneficial in patients with both SIBO and IBS as it is efficacious in IBS.

The clinician should be vigilant about the bacterial resistance and side effects when considering and selecting antibiotic management.


These agents may be useful in SIBO patients. One pilot trial evaluated the outcome of Lactobacillus casei Shirota in patients with SIBO diagnosed by a positive hydrogen test. Following a 6-week period of therapy with this probiotic, 64% of the patients exhibited a negative breath test although symptomatic improvement was not remarkable.

Another pilot investigation compared probiotic use versus metronidazole therapy. The trial noted that probiotics demonstrated greater success in symptom management, in comparison to metronidazole. To corroborate this result, a randomized, double-blinded placebo controlled investigation is necessary to provide further information.

Fluids and nutrition

Patients suffering from dehydration and malnourishment may require treatment with intravenous fluids and TPN.


Since vitamin deficiencies and iron deficiency anemia may occur in SIBO patients, these should be corrected. These vitamins include the fat-soluble ones and B12.

Also, the proper assessment and management of osteoporosis are warranted, as this is a recognized complication of SIBO.


The prognosis of SIBO is usually related to the cause of the condition and other factors, such as the ensuing consequences.

The most common cause of death is liver failure due to the parenchymal destruction in this organ. Other reasons linked to the fatality of SIBO patients are the decreased venous access or complications of severe sepsis.

Pharmacological bowel compensation can replace the long-term parenteral nutrition therapy. Surgical intervention that does not involve transplantation may improve SIBO in almost 80% of cases.

There is a high mortality rate with the post-surgical complications. In survivors, up to 90% will remain alive after one year and about 60% will reach the 4-year mark.

In the newborn population receiving total parenteral nutrition (TPN), almost 70% will achieve a 4-year survival rate while about 20% will reach the 5-year survival point.


The causes of SIBO are typically convoluted, as it is related to many diseases that affect the physiologic antibacterial mechanisms. These endogenous processes that restrict the growth of bacteria are 1) intestinal motility, 2) gastric acid secretion, 3) the ileocecal valve, 4) the presence of antibiotic substances in pancreatic and biliary secretions, and 5) the presence of immunoglobulins in intestinal secretions [4].

The disorders that affect these mechanisms may lead to SIBO. For example, etiologies of this condition include motility disorders such as diabetes-induced autonomic neuropathy, scleroderma, etc. Additionally, anatomical defects such as the resection of the ileocecum, small bowel obstruction, fistulas, diverticula, and surgical loops can cause bacterial overgrowth. Finally, achlorhydria and pancreatic exocrine insufficiency may contribute to the development of SIBO, as do immunodeficiency diseases.

Note that small bowel motility disorders and chronic pancreatitis account for 90% of cases [5].

The causes and risk factors may be the same in patients. Also, some individuals have numerous predisposing factors for SIBO. Adding to the complexity of the condition, the underlying pathology may contribute to the development of SIBO, which in turn complicates the disease further.


The prevalence of SIBO, in general, has not been established. This condition is typically under-diagnosed, as it does not always cause symptoms, and when it does, they are nonspecific or are attributed to underlying disorders.

Certain investigations evaluated the occurrence of SIBO. The condition was observed in 2.5% to 22% in studies that used healthy subjects as the control [6]. Also, the frequency of SIBO varies from one disease to another according to literature. For example, 30% to 85% of patients with irritable bowel syndrome (IBS) have SIBO [7]. Bacterial overgrowth is found in up to 50% of celiac disease cases [8], greater than 50% of patients with liver cirrhosis [9], and 90% of elderly individuals with lactose intolerance [10]. Additionally, one investigation reported that the condition was demonstrated in 17% of asymptomatic obese patients versus 2.5% of non-obese subjects [11].

Sex distribution
Age distribution


The antibacterial mechanisms that control bacterial growth can be disrupted when there is decreased gastric acid secretion or small bowel immobility. Regarding the latter, the migrating motor complex (MMC) is responsible for the flow of bacteria into the large bowel during periods of fasting,

Other protective mechanisms include the functional ileocaecal valve, the production of immunoglobulins in intestinal secretions and antibacterial properties in pancreatic and biliary secretions.

Intestinal dysmotility

Patients with diabetes and scleroderma may exhibit difficulty with small bowel motility. Hence, these diseases prevent the migration of the bacteria into the large intestine.

Anatomic defects

Procedures such as a gastrectomy can create loops of small bowel that house excess bacteria.

Pathologies such as Crohn disease and post-surgical residuals may lead to obstruction or pockets that foster an environment of bacterial overgrowth.


Immunodeficient individuals exhibit a high prevalence of SIBO. These patients have profoundly elevated immunoglobulin A in the duodenal and jejunal mucosa.

Findings in SIBO

Excessive production of bacteria can activate an inflammatory reaction in the mucosal layer of the bowel. This may be demonstrated in microscopic examination, although this is not always necessary [12]. Furthermore, the biopsy findings associated with SIBO in elderly patients are blunting of the villi, thinning of crypts and the mucous layer and increased amounts of lymphocytes [13]. These changes are corrected with antibiotic therapy [13].


The recurrence of SIBO is common, since the elimination of the overgrowth will not cure the underlying disease.

Treatment with probiotics or antibiotics does not prevent the relapse, as bacteria can accumulate within 2 weeks of completion of these agents. Therefore, one protocol outlines preventive strategies, which include 1) the use of a pro-motility drug to stimulate the MMC, 2) adherence to a continuous SIBO diet, low in carbohydrates, 3) treatment of coexisting diseases contributing to SIBO, 4) patients with Hydrochloric Acid (HCl) deficiency should receive supplementation with this acid, 5) withdrawal of proton pump inhibiting drugs (PPIs) and antacids, 6) treatment of neurological disorders, and 7) repair of Ileocecal Valve Syndrome (IVC) to prevent the bacterial backflow into the small bowel.

Note that prokinetic drugs and a proper diet are crucial in the prevention of SIBO recurrence.


Small intestinal bacterial overgrowth (SIBO) is characterized by excessive numbers and/or change in the type of bacteria in an organ. The complex flora of the human gastrointestinal tract features a delicate balance that is protected by normal physiologic and anatomical mechanisms. Hence, any disruption to these processes can result in serious alterations in the health of the patient. Furthermore, the etiology is typically complicated and may be associated with various factors.

The clinical presentation may fluctuate, as some patients will not exhibit symptoms while others feature manifestations such as weight loss, diarrhea, abdominal pain, and bloating. Additionally, SIBO may give rise to complications such as osteoporosis and fat-soluble vitamin deficiencies.

The clinical assessment for patients suspected to have SIBO consists of a detailed medical and surgical history, physical exam, and particular studies, such as the gold standard investigation of jejunal aspirates. Moreover, the criteria for diagnosis is the result of 10^5 bacteria or more per milliliter of aspiration [1] [2] [3]. Other tests include non-invasive methods, such as breath tests.

The therapeutic goal is to treat the cause, if possible. The exact management is tailored for the particular patient and may warrant the use of antibiotics and/or probiotics. Additionally, vitamin and nutritional deficiencies, as well as other sequelae should be addressed.

Patient Information

Small intestine bacterial overgrowth (SIBO) is a disorder described by the production of large bacterial populations in the small intestine.

What are the causes of SIBO?

There are numerous conditions and diseases that can cause this excessive growth of bacteria in the small intestine such as:

  • Diabetes and scleroderma, which cause trouble with the movement of the small bowel. Therefore, the diseases can prevent the bacteria from migrating from the small intestine into the large intestine.
  • AIDS and other immunodeficiency diseases can prevent clearance of the bacteria.
  • Short bowel syndrome occurs when a segment of the small intestine is removed.
  • Post-surgical complications that cause blockage in the small intestine.
  • Surgeries that develop loops of the small intestine that allow growth of bacteria.
  • Irritable bowel syndrome (IBS).

What are the symptoms?

In addition to weight loss, the patients may experience gastrointestinal disturbances such as:

What are some of the complications?

Normally, the small intestine does not have large numbers of bacteria like the large intestine does. Therefore, the many bacteria use up nutrients and vitamins that the body would otherwise use for itself. This is why patients with SIBO will become malnourished. Patients may also develop dehydration, liver disease, and osteoporosis.

How is this condition diagnosed?

The clinician will evaluate the signs and symptoms and assess the full medical and surgical history. Also, they will perform a physical exam and obtain important test, such as small intestine biopsy and aspirates, breath tests, abdominal x-rays, stool fat test, complete blood count (CBC), blood chemistry levels, and vitamin levels.

How is SIBO treated?

The aim of the treatment is to target the overgrowth of the bacteria and is usually tailored to the specific patient. This may consist of antibiotics, probiotics, and/or medications that increase the movement in the small intestine. These patients are also encouraged to follow a specific diet with low amounts of carbohydrate.

Another aspect of the therapy includes providing the patients with fluids and nutrition. Dehydrated and malnourished patients should be treated with intravenous fluids and total parenteral nutrition (TPN).

How can SIBO be prevented?

Promotility drugs can help to prevent further episodes of this condition from developing. Also, a SIBO friendly diet is considered important. The doctor may decide to take other measures such as stopping antacids and maybe even surgery to repair anatomical abnormalities.



  1. Toskes PP, Kumar A. Enteric bacterial flora and bacterial overgrowth syndrome. In: Feldman M, Scharschmidt BF, Sleisenger MH, editors. Sleisenger & Fordtran’s Gastrointestinal and Liver Disease. 6th ed. Philadelphia: WB Saunders; 1998. pp. 1523–1535.
  2. Gasbarrini A, Lauritano EC, Gabrielli M, et al. Small intestinal bacterial overgrowth: diagnosis and treatment. Digestive diseases. 2007;25(3):237-40.
  3. Khoshini R, Dai SC, Lezcano S, Pimentel M. A systematic review of diagnostic tests for small intestinal bacterial overgrowth. Digestive Diseases and Sciences. 2008;53(6):1443–1454.
  4. Lewis SJ, Franco S, Young G, O'Keefe SJ. Altered bowel function and duodenal bacterial overgrowth in patients treated with omeprazole. Alimentary Pharmacology and Therapeutics. 1996;10(4):557–561.
  5. Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. American Journal of Clinical Nutrition. 1999;69(5):1035S–1045S.
  6. Grover M, Kanazawa M, Palsson OS, et al. Small intestinal bacterial overgrowth in irritable bowel syndrome: association with colon motility, bowel symptoms, and psychological distress. Neurogastroenterology and Motility. 2008;20(9):998–1008.
  7. Lin HC. Small intestinal bacterial overgrowth: a framework for understanding irritable bowel syndrome. Journal of American Medical Association. 2004;292(7):852–858.
  8. Rubio-Tapia A, Barton SH, Rosenblatt JE, Murray JA. Prevalence of small intestine bacterial overgrowth diagnosed by quantitative culture of intestinal aspirate in celiac disease. Journal of Clinical Gastroenterology. 2009;43(2):157–161.
  9. Pande C, Kumar A, Sarin SK. Small-intestinal bacterial overgrowth in cirrhosis is related to the severity of liver disease. Alimentary Pharmacology and Therapeutics. 2009;29(12):1273–1281.
  10. Almeida JA, Kim R, Stoita A, McIver CJ, Kurtovic J, Riordan SM. Lactose malabsorption in the elderly: role of small intestinal bacterial overgrowth. Scandinavian Journal of Gastroenterology. 2008;43(2):146–154.
  11. Sabaté JM, Jouët P, Harnois F, et al. High prevalence of small intestinal bacterial overgrowth in patients with morbid obesity: a contributor to severe hepatic steatosis. Obesity Surgery. 2008;18(4):371–377.
  12. Riordan SM, McIver CJ, Wakefield D, et al. Small intestinal mucosal immunity and morphometry in luminal overgrowth of indigenous gut flora. American Journal of Gastroenterology. 2001;96(2):494–500.
  13. Haboubi NY, Lee GS, Montgomery RD. Duodenal mucosal morphometry of elderly patients with small intestinal bacterial overgrowth: Response to antibiotics treatment. Age Ageing. 1991;20(1):29–32.

Ask Question

5000 Characters left Format the text using: # Heading, **bold**, _italic_. HTML code is not allowed.
By publishing this question you agree to the TOS and Privacy policy.
• Use a precise title for your question.
• Ask a specific question and provide age, sex, symptoms, type and duration of treatment.
• Respect your own and other people's privacy, never post full names or contact information.
• Inappropriate questions will be deleted.
• In urgent cases contact a physician, visit a hospital or call an emergency service!
Last updated: 2019-07-11 19:59