[1] Patients with bacterial overgrowth typically develop symptoms which may include nausea, bloating, vomiting, diarrhea, malnutrition, weight loss, and malabsorption[2] by various mechanisms.

The diagnosis of bacterial overgrowth is made by a number of techniques, with the gold standard[3] being an aspirate from the jejunum that grows in excess of 105 bacteria per millilitre.

[4] Bacterial overgrowth can cause a variety of symptoms, many of which are also found in other conditions, making the diagnosis challenging at times.

[4] Anemia may occur from a variety of mechanisms, as many of the nutrients involved in production of red blood cells are absorbed in the affected small bowel.

[10] Some studies reported up to 80% of patients with irritable bowel syndrome (IBS) have SIBO (using the hydrogen breath test).

First, the excessive bacterial concentrations can cause direct inflammation of the small bowel cells, leading to an inflammatory diarrhea.

These factors can be grouped into four categories: (1) motility disorders, impaired movement of the small bowel, or anatomical changes that lead to stasis (a state in which the normal flow of a body liquid stops); (2) disorders of the immune system; (3) interference with the production of proteolytic enzymes, gastric acid, or bile; and (4) conditions that cause more bacteria from the colon to enter the small bowel.

[4] In some people, methanogens may reside in the oral cavity, as evidenced by reductions in breath methane levels following mouthwash with chlorhexidine.

[17] There is an overlap in findings between tropical sprue, post-infectious irritable bowel syndrome and small intestinal bacterial overgrowth in the pathophysiology of the three conditions and also SIBO can similarly sometimes be triggered by an acute gastrointestinal infection.

[18][19][20] As of 2020, there is still controversy about the role of SIBO in the pathogenesis of common functional symptoms such as those considered to be components of irritable bowel syndrome.

[22] After surgery involving the stomach and duodenum (most commonly with Billroth II antrectomy), a blind loop may be formed, leading to stasis of flow of intestinal contents.

[24] The use of proton pump inhibitors, a class of medication used to reduce stomach acid, is associated with an increased risk of developing SIBO.

[citation needed] After bariatric surgery for obesity, connections between the stomach and the ileum can be formed, which may increase bacterial load in the small bowel.

[citation needed] However, some physicians suggest that if the suspicion of bacterial overgrowth is high enough, the best diagnostic test is a trial of treatment.

[4] SIBO may be defined as an increased number of bacteria measured via exhaled hydrogen and/or methane gas following the ingestion of glucose, or via analysis of small bowel aspirate fluid.

Future advances in sampling technology and techniques for counting bacterial populations and their metabolites should provide much-needed clarity.

Production of methane therefore, may not be bacterial, nor limited to the small intestine, and it has been proposed that the condition should be classified as a separate 'intestinal methanogen overgrowth' (IMO).

[29] Treatment strategies should focus on identifying and correcting the root causes, where possible, resolving nutritional deficiencies, and administering antibiotics.

[4] Lactobacillus casei has been found to be effective in improving breath hydrogen scores after six weeks of treatment presumably by suppressing levels of a small intestinal bacterial overgrowth of fermenting bacteria.

[32][non-primary source needed] A combination of probiotic strains has been found to produce better results than therapy with the antibiotic drug metronidazole.

[38] For example, if the symptoms are caused by bacterial overgrowth feeding on indigestible carbohydrate rich foods, following a FODMAP restriction diet may help.