The microbial ecosystem that occupies the human intestine is essential for the maintenance of health. An intricate relationship exists between the gut microbiome, the central nervous system, the neuroimmune and neuroendocrine systems, the autonomic nervous system, and the enteric nervous system, the interplay of which is responsible for the effective control of the gut by the higher centers. The development of new techniques that enable better characterization of gut bacteria has noticeably increased interest how the human microbiome affects the development of disease, particularly so in the pathophysiology of functional gastrointestinal disorders, where epidemiological studies have long-linked acute gut infection with the development of chronic functional symptoms. Up to 30 % of patients develop irritable bowel syndrome (IBS) after suffering from a gastrointestinal infection, and 40 % describe symptomatic benefit from antibiotic therapy [1]. IBS has also been associated with altered diversity and composition of gut bacteria [2]. Although the exact mechanisms remain poorly defined, the gut microbiome is firmly associated with IBS pathogenesis. Given the presumed pathogenic role of the gut microbiota in IBS, its manipulation is now a ‘‘hot’’ topic in management, from the addition of ‘‘good bacteria’’ via probiotics, the promotion of ‘‘good bacteria’’ via prebiotics, the change of bacterial populations by antibiotics, and the replacement of bacteria via fecal microbiota transfer. Antibiotics have received the most attention since they are a major therapeutic tool in treating small intestinal bacterial overgrowth (SIBO), postulated to be an important link between gut bacteria and IBS. The small bowel normally contains only a fraction of the bacteria present in the large bowel (10 4 ‐10 8 vs. 10 9 ‐10 12 )[ 3]. SIBO, defined as an excess of colonic-type bacteria in the small bowel, is often diagnosed in patients with small bowel abnormalities such as altered anatomy, motility, or flow resulting in stasis, enhancing bacterial proliferation. While SIBO provides an attractive (and potentially treatable) cause for the symptoms of IBS, in reality diagnosing SIBO in IBS patients who have normal anatomy is fraught with controversy.