The majority of microbiome studies focus on stool, which is broadly reflective of the GI microbiome, and the colonic mucosa, where microbes may play a role in triggering inflammation 3. Its role in modulating important physiological processes such as GI motility and secretion, maintenance of epithelial barrier integrity, and its role in communication between the gut and the central nervous system may underlie its contribution to symptoms associated with FGIDs such as irritable bowel syndrome (IBS) 1, 2. The human gut microbiome has emerged as an important factor in the pathogenesis of functional gastrointestinal (GI) disorders (FGIDs). Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics.
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