Abstract
Small intestinal bacterial overgrowth (SIBO) is highly prevalent and is associated with numerous gastrointestinal disorders, but the microbes involved remain poorly defined. Moreover, existing studies of microbiome alterations in SIBO have utilized stool samples, which are not representative of the entire gastrointestinal tract. Therefore, we aimed to determine and compare the duodenal microbiome composition in SIBO and non-SIBO subjects, using duodenal aspirates from subjects undergoing standard-of-care esophagogastroduodenoscopy without colon preparation. Using the recently-redefined cutoff for SIBO of >103 colony forming units per milliliter (CFU/mL), 42 SIBO and 98 non-SIBO subjects were identified. Duodenal samples from SIBO subjects had 4x103-fold higher counts than non-SIBO subjects when plated on MacConkey agar (P<0.0001), and 3.8-fold higher counts when plated on blood agar (P<0.0001). Twenty subjects had also undergone lactulose hydrogen breath tests (LHBTs), of whom 7/20 had SIBO. At the 90-minute timepoint, 4/7 SIBO subjects had positive LHBTs (rise in hydrogen (H2) ≥ 20 ppm above baseline), as compared to 2/13 non-SIBO subjects. 16S ribosomal RNA (rRNA) sequencing revealed that SIBO subjects had 4.31-fold higher relative abundance of Proteobacteria (FDR P<0.0001) and 1.64-fold lower Firmicutes (P<0.0003) than non-SIBO subjects. This increased relative abundance of Proteobacteria correlated with decreased α-diversity in SIBO subjects (Spearman R = 0.4866, P<0.0001) Specific increases in class Gammaproteobacteria correlated with the area-under-the-curve for H2 for 0–90 mins during LHBT (R = 0.630, P = 0.002). Increases in Gammaproteobacteria resulted primarily from higher relative abundances of the family Enterobacteriaceae (FDR P<0.0001), which correlated with the symptom of bloating (Spearman R = 0.185, 2-tailed P = 0.028). Increases in family Aeromonadaceae correlated with urgency with bowel movement (Spearman R = 0.186, 2-tailed P = 0.028). These results validate the >103 CFU/mL cutoff for the definition of SIBO, and also reveal specific overgrowth of Proteobacteria in SIBO vs. non-SIBO subjects, coupled with an altered Proteobacterial profile that correlates with symptom severity. Future research may elucidate host-microbiome interactions underlying these symptoms in SIBO patients.
Highlights
Small intestinal bacterial overgrowth (SIBO) is a condition defined by abnormal and excessive numbers of bacteria in the small bowel, usually associated with gastrointestinal (GI) symptoms such as bloating, excess of gas, abdominal discomfort, diarrhea, and weight loss [1, 2]
A total of 98 subjects were defined as non-SIBO, based on bacterial counts 103 colony forming units per milliliter (CFU/mL) for duodenal aspirates (DA) when plated on MacConkey agar
These techniques were used to explore the microbial populations of the small intestine and identify how these are altered in SIBO
Summary
Small intestinal bacterial overgrowth (SIBO) is a condition defined by abnormal and excessive numbers of bacteria in the small bowel, usually associated with gastrointestinal (GI) symptoms such as bloating, excess of gas, abdominal discomfort, diarrhea, and weight loss [1, 2]. SIBO has been defined by two primary methods; direct culture of small bowel aspirates [11], and indirect assessment using carbohydrate (e.g. lactulose, glucose) breath testing [12, 13]. In their current forms, both tests provide only a narrow understanding of the composition of the small intestinal microbiome or its impact on the host. Despite the limitations of these diagnostic approaches, there is no doubt that patients with common conditions respond to antibiotics, supporting a role for the microbiome in certain conditions and even leading to approval by the United States Food and Drug Administration (FDA) of an antibiotic for the treatment of IBS [20]
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