OBJECTIVES The composition of the small intestinal microbiota has not yet been characterized thoroughly using culture-independent techniques. We compared small intestinal microbial communities in patients with and without small intestinal bacterial overgrowth (SIBO) using culture-dependent and culture-independent bacterial identification approaches. METHODS Small bowel aspirate and mucosal samples were collected from patients with suspected SIBO. The aspirates were cultured to diagnose SIBO, defined as ≥10 colony-forming units/mL coliform or ≥10 colony-forming units/mL upper aerodigestive tract bacteria. Bacteria in the aspirates and mucosa were identified using 16S rRNA gene sequencing. We compared small intestinal microbiome composition between groups with and without a culture-based SIBO diagnosis. RESULTS Analysis of the aspirate and mucosal microbial communities from 36 patients revealed decreased α-diversity but no differences in β-diversity in patients with SIBO compared with those without SIBO. There were no significant differences in the relative abundance of individual taxa from the aspirates or mucosa after adjustment for false discovery rate between patients with and without SIBO. Subgroup analysis revealed significant differences in mucosal β-diversity between the coliform and upper aerodigestive tract subgroups. Relative abundances of a mucosal Clostridium spp. (P = 0.05) and an aspirate Granulicatella spp. (P = 0.02) were higher in coliform SIBO vs non-SIBO subgroups. The microbial composition and relative abundance of multiple taxa significantly differed in the mucosal and aspirate specimens. DISCUSSION Culture-based results of small bowel aspirates do not correspond to aspirate microbiota composition but may be associated with species richness of the mucosal microbiota.

中文翻译：

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怀疑小肠细菌过度生长的患者近端小肠菌群的特征：一项跨部门研究。

目的尚未使用与培养无关的技术来彻底表征小肠微生物群的组成。我们使用依赖于培养物和不依赖于培养物的细菌鉴定方法，比较有无小肠细菌过度生长（SIBO）患者的小肠微生物群落。方法从疑似SIBO患者中收集小肠抽吸物和粘膜样品。培养吸出物以诊断SIBO，SIBO定义为≥10个菌落形成单位/ mL大肠菌群或≥10个菌落形成单位/ mL上呼吸道细菌。使用16S rRNA基因测序鉴定出吸出物和粘膜中的细菌。我们比较了有无基于文化的SIBO诊断的组之间的小肠微生物组组成。结果对36例患者的吸出物和黏膜微生物群落进行分析后发现，与无SIBO的患者相比，SIBO患者的α多样性降低，但β多样性无差异。在对有和没有SIBO的患者进行假发现率调整后，从吸出物或粘膜得到的单个分类单元的相对丰度没有显着差异。亚组分析显示大肠菌群和上消化道亚群之间的粘膜β多样性存在显着差异。粘膜梭状芽胞杆菌的相对丰度。（P = 0.05）和吸出的Granulicatella spp。大肠菌群SIBO组（P = 0.02）高于非SIBO亚组。在粘膜和抽吸组织中，多种类群的微生物组成和相对丰度明显不同。