Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth: A Cross-Sectional Study.

Small intestinal bacterial overgrowth (SIBO) has historically been described in the context of maldigestion and malabsorption in patients with anatomic abnormalities (e.g., fistulae, strictures, bowel reconstruction, bowel obstruction), underlying dysmotility secondary to diabetes or scleroderma, and hypochlorhydria (1). This syndrome has also been implicated in the pathophysiology of numerous gastrointestinal and hepatobiliary diseases including common conditions such as irritable bowel syndrome (IBS) (2) and functional dyspepsia (3). Typical SIBO-associated symptoms include bloating, diarrhea, abdominal pain, and gas. SIBO symptoms may overlap with those of functional gastrointestinal disorders. However, the role of SIBO in the pathogenesis of functional gastrointestinal disorders remains controversial given that its definition relies on tests, including breath test and culture of small bowel aspirates, which have not been appropriately validated (4). Indirect techniques such as breath testing have important limitations related to heterogeneous testing methods and lack of standardization in interpretation. To address these limitations, guidelines for breath testing indications, performance, and interpretation were recently published in a North American consensus document (5). Yet, there remain important knowledge gaps in how these tests reflect the microbial landscape of the human small intestine. Small bowel aspirates and culture were previously considered the gold standard for the diagnosis of SIBO. SIBO has traditionally been defined by abnormally high amounts of bacteria in the small intestine and more precisely by >105 colony-forming units (CFU)/mL of colonic-type bacteria from jejunal aspirates (6). However, the validity of this approach has been questioned as the proposed cutoff of 105 seemed more predictive of postsurgical patients in a previous systematic review (7). Others have suggested that lower cutoff values of 103 CFU/mL be considered as diagnostic of SIBO (5), especially if coliforms are present (8). Standard culture-based techniques are limited in their ability to characterize fully the complex diversity of the small intestinal microbiome, particularly as a large proportion of bacterial species remain uncultured (9). In light of increasing evidence supporting the hypothesis that the intestinal microbiome serves a key role in host physiology and gastrointestinal disease, better characterization of the small intestinal microbiome will be a critical step in developing novel diagnostic and therapeutic strategies in a number of human diseases and disorders. In the recent years, the introduction of culture-independent techniques has dramatically expanded our ability to characterize the complexity of the intestinal microbiota. It also has increased our knowledge of the culture conditions needed to detect and identify previously difficult to culture organisms (10). Integration of rapid molecular approaches (11) for the assessment of SIBO in conditions such as IBS has yielded promising data including evidence for decreased microbial diversity from duodenal aspirates in patients with IBS compared with control subjects (12). However, these findings are preliminary. Overall, there are limited data reporting detailed characterizations of the human small intestinal microbiome. It may be hypothesized that alterations in the small intestinal microbiome are associated with culture-proven SIBO, which in turn could suggest that although imperfect, culture-proven SIBO is at least a useful surrogate marker of small intestinal dysbiosis. However, further investigation is needed to (i) explore the role of microbial diversity in SIBO using culture-independent approaches and (ii) describe the interactions between the host and small intestinal microbiome in the context of gastrointestinal disease. This study characterizes small intestinal microbial composition of small bowel aspirates and mucosal specimens in patients with and without a diagnosis of SIBO defined by qualitative and quantitative culture of proximal small bowel aspirates.